Genetic features of suspension bluefin tuna cells

Abstract

Provided herein are altered cell lines comprising a suspension cell line adapted from an adherent cell line having a different expression profile from a corresponding non-altered adherent cell line, methods for generating altered cell lines, and methods of characterizing altered expression profiles for a gene, a transcript, or a protein in an altered cell line.

Description

GENETIC FEATURES OF SUSPENSION BLUEFIN TUNA CELLSCROSS REFERENCE TO RELATED APPLICATIONS

[0001] This application claims priority from U.S. provisional application No.: 63 / 647,295 filed on May 14, 2024, the contents of which are incorporated by reference in its entirety.FIELD

[0002] This present disclosure provides methods and uses for generating altered cell lines, such as a suspension cell line. Also provided are compositions of altered cells, such as compositions comprising suspension cell lines.BACKGROUND

[0003] Global consumption of meat continues to surge as demand is driven upward by population growth, individual economic gain, and urbanization (Godfray, H. C. J. et al.). In 2012, the Food and Agriculture Organization (FAO) of the United Nations projected the global demand for meat would reach 455 M metric tons by 2050, which is a 76% increase from 2005 (Alexandratos, N. & Bruinsma). Likewise, the global demand for fish is projected to reach 140 M metric tons by 2050.

[0004] Food produced using animals is inefficient, as the animals consume large amounts of food throughout their lives, of which 80-90% of the calories are wasted on the animal’s metabolism and the production of non-edible tissues. Also, current methods of large-scale animal husbandry are linked to public health issues, environmental degradation, and animal welfare concerns. Consequently, removing animals from the manufacturing process may help alleviate some of the issues noted above.

[0005] Cellular agriculture is defined as the production of agricultural products from cell cultures rather than from whole plants or animals. Biomedical engineering developments such as closed-system bioreactor production of land animal cells create a basis for the large- scale production of marine animal cells.

[0006] With oceans at risk, cell-based seafood production provides a unique opportunity to transform the sustainability landscape. The concept of producing seafood from fish cell cultures is emerging as a means to address public health, environmental, and animal welfare challenges of animal agriculture.

[0007] Cell-based food production involves culturing cells isolated from animals, plants or microorganisms, followed by processing to generate food products that are comparable tothe corresponding conventional food products, including meat, poultry and aquatic products. The concept of producing meat from cell cultures rather than from whole animals as a means to provide nutritional muscle tissue is detailed in a paper authored by Datar, I., and Betti, M. (2010). The discussion therein emphasizes that cellular agriculture could be extended to fish, mollusk, and crustacean cells and tissues to replace seafoods. A defining feature of using fish cell-based production systems is its potential beneficial impact on sustainability, considering that cell-based seafood could lead to greater preservation of marine environments.

[0008] The physiological properties of fish cell culture may be uniquely suited to cultivation in vitro. These physiological properties, including tolerance to hypoxia, high buffering capacity, and low-temperature growth conditions, make marine cell culture an attractive opportunity for scaled production of cell-based seafood. These features also present a great opportunity for cell-based seafood production via bioreactor cultivation (Rubio et al., 2019).

[0009] Growth and maintenance of cell mass in the adherent system for cell-based seafood production is logistically challenging since the attachment-dependent culture processing generally requires more resources, steps, and time than suspension. As a result, the scale-up of adherent cell culture process is complicated and labor intensive. Currently, these issues are minimally mitigated by using microcarrier technology, which employs small beads of glass, plastic, or other synthetic or natural materials of various densities, porosities, and surface treatments dispersed in a suspension within stirred tank reactors. In the cell-based seafood industry, several compositions of edible microcarriers are being developed and tested to maximize attachment and proliferation. To achieve cell-expansion in such a system would require rigorous testing of several types of materials for adherence and proliferation potential of cells. Adding the cost of using a successful microcarrier in each production run would still make it a less viable option.

[0010] Cell lines are conventionally grown in serum-containing media to aid growth and proliferation of the cells. However, serum is not advantageous, particularly in large-scale commercial production, due to its high cost, risk of contamination, undefined nature, and variability.

[0011] Adaptation of cells to grow in suspension would accelerate all the above- mentioned steps, improve process scale-up significantly, and therefore, reduce the production cost. The challenges to solve during the adaptation process include low cell viability, relatively longer cell doubling time and slower growth rate.

[0012] A suspension process also has the advantage of being easier to operate than an adherent one. Adherent processes require cells to be disassociated from their growth surface for routine maintenance, scale-up, and counting. Dispensing of this step greatly simplifies the process. Once the cell line is no longer dependent on a surface for growth, scale-up becomes much easier and the range of technology to support manufacture increases.

[0013] Therefore, there is a need in the art for a suspension cell line derived from fish cells that have one or all of the following characteristics: replicates continuously in suspension as single cells making them ideal for use in large-scale bioreactors; grows to high density with a high degree of viability; thrives in serum- free medium.

[0014] Therefore, there is a need in the art for a suspension cell line that can grow continuously as single cell suspensions in a commercial serum-free medium, and divide rapidly.BRIEF SUMMARY

[0015] In some aspects, the present disclosure relates to the adaptation of adherent cell lines to metabolically intact and stable altered fish cell lines that can be grown in suspension culture without adherence to supporting material. Included is a method to obtain the altered cell line from adherent Bluefin tuna (BFT) cells. The altered cell lines are self-renewing; grow in suspension as single cells; are capable of replicating in a serum or serum- free medium; are stable; can be propagated continuously for at least 4 months and 50 population doublings; and are free of any detectable adventitious agents including mycoplasma, bacteria, and viruses, including retroviruses.

[0016] In some aspects, the present disclosure further relates to BFT myoblast cells lines that have been altered to grow and proliferate in suspension conditions. The suspension cell lines were generated by mutagenesis of the parent adherent cell lines and adapted to suspension conditions in a shaker flask. The ability to generate altered cell lines that grow in suspension conditions represents a significant technological advance in the field of cell-based seafood agriculture.

[0017] In certain aspects, the present disclosure further relates to altered expression profiles identified in the suspension cell lines and methods of characterizing altered expression profiles. Altered expression profiles comprise both upregulation and downregulation of genes, transcripts, or proteins of at least 329 unique genes that were identified as being altered.

[0018] In some aspects, described herein are compositions and methods for generating an altered cell line. The altered cell line composition may be a suspension cell line. The altered cell line composition may be derived from fish cells, such as BFT cells. The altered cell line composition may be derived from myoblasts, myocytes, adipocytes, fibroblasts, keratinocytes, epithelial cells, endothelial cells, embryonic derived cells, induced pluripotent stem cells, or mesenchymal stem cells.

[0019] In some aspects, provided herein are compositions wherein the composition may comprise an altered cell line that has an altered expression profile as compared to an expression profile of a corresponding non-altered cell line, wherein the altered cell line is a suspension cell line. Also provided herein are compositions wherein the composition may comprise an altered cell line that has an altered expression profile as compared to an expression profile of a reference non-altered cell line, wherein the altered cell line is a suspension cell line.

[0020] In some embodiments, the altered expression profile comprises an altered gene expression profile and / or an altered phenotypic profile. In some embodiments, the altered phenotypic profile comprise of improved viability and stable growth rates in (1) nonadherent, suspension cell culture, (2) serum-free media cell culture, and / or (3) animal component-free media cell culture.

[0021] In some variations, the altered cell line composition may have an altered expression profile as compared to an expression profile of a corresponding non-altered cell line. In some embodiments, the altered expression profile comprises an upregulated gene expression profile. In some embodiments, the altered expression profile comprises a downregulated gene expression profile.

[0022] In some embodiments, the altered expression profile comprises an upregulated gene expression profile. In some embodiments, the altered expression profile comprises a downregulated gene expression profile.

[0023] In some embodiments, the altered cell line composition may have an altered expression profile that comprise a gene, a transcript, or a protein selected from the group consisting of ABCG2, SI, NDUFS8, ITGA5, CNTD1, PKHD1L1, PLXNB2, CASP10, FN1, ASAP2, IL13RA2, DAAM2, MCTP1, NUGGC, MEGF10, KIAA1324L, CPXM1, PHACTR4, FGF13, FLT1, PRICKLEI, ZEB1, SULF2, NET1, KIFAP3, HDAC9, DOPEY2, MAN2B2, TLE4, GARNL3, PFKP, ANKS1B, ABHD4, GTPBP2, PLXNA3, CREB3, NLRP12, PTPRK, RGN, GLUL, ABCG2, SI, MMP13, CMYA5, CAMTAI, ABCA1, CDH1, NDUFS8, EPHA10, DCHS1, OLFML1, ITGA5, SLC12A5, F8, CNTD1, PKHD1L1,ARHGAP22, LTBP3, PPP1R42, ADH5, REEP1, ADAMTS1, ATF5, ALDH1L1, ADAMTSL3, PLXNB2, CASP10, CSF1R, BSCL2, SLC15A2, CYP3A4, FN1, KIAA1644, ABCC6, GARS, ANTXRL, ASAP2, GGT7, GARS, P2RY4, ABCA1, IL1B, PRKAG2, TNFAIP3, VASP, FSTL1, IL13RA2, KLHL38, SLC47A2, SLC5A5, FKBP14, MAGI2, GTPBP1, DAAM2, EXOC3L1, RAB37, KRT12, SLCO2B1, ADM2, MCTP1, DACT2, NUGGC, CHRD, ROBO3, MMP19, PTK7, PLEKHH1, MEGF10, FERMT1, SRPX2, TOX3, CTSS, MST1R, CCDC1O8, SEMA6C, AVPR1A, TSC22D4, FSTL3, ITGA2, PTGIS, COLEC12, KIAA1324L, NLN, FBXO32, CCDC153, CPXM1, PHACTR4, FGF13, DOCKIO, CYSTM1, FAM214A, CAND2, ARHGEF25, PTPLAD2, PAMR1, ULK2, PRODH, KRT8, TRIM55, KIAA1522, OPLAH, PREXI, LRP2, TBC1D2, INVS, FLT1, PRICKLEI, ADAMTS12, MDM2, CSRNP1, RTP4, MED13L, NFKBIA, RGS12, LMNA, RIN1, TCN2, PDE7B, COL23A1, KIAA0141, ANTXRL, AATK, ZEB1, IL1RAP, COL23A1, SULF2, MXRA8, ZMIZ1, TMTC2, KIFAP3, ISG15, MAP6, HDAC9, ACSL3, DOPEY2, MAN2B2, GARNL3, MKL2, ATXN1, WDFY2, CAPN2, ERRFI1, FARP1, HFE2, ZC3H12D, PFKP, ANKS1B, UAP1L1, ABHD4, RNF165, MPP5, SAT1, HBP1, AMPD2, HOMEZ, B3GNT2, GTPBP2, STEAP4, PCDHAC2, COL4A3BP, TNS3, RNF169, AEBP1, TFE3, TTYH1, NEIL1, KIAA1033, MMP14, ACSL4, KLHL40, LPIN1, FGD1, XPC, PLXNA3, TNFAIP2, CCDC92, DAB2, MTMR11, ZFYVE28, PC, ADIPOR2, MYODI, ZBTB33, METRNL, TBC1D2B, MFAP5, SCD, PPP1R3C, VPS4B, QPCT, METRNL, CTSH, CREB3, ARHGAP24, WDFY4, ROR2, ATP6V1B2, CTSZ, CXADR, MFSD2A, AVIL, XKRX, NLRP12, PTPRK, CHRNG, TIFA, TMCC3, SEMA4B, GDF10, PARD3, RGN, MAN2B1, PNPLA6, COL15A1, VPS41, TBC1D26, GHDC, ATHL1, NUGGC, TBC1D26, FSTL3, PNPLA6, XKRX, LTBP3, MFAP5, ABCC6, CSF1R, FARP1, SRPX2, LRP2, AATK, KRT12, MCTP1, CCDC153, SLC5A5, KRT8, PAMR1, FN1, HEY1, SCUBE3, MYLPF, MARCKSL1, RAB11FIP1, NTN1, GPT, GPD1, BAIAP2, MFI2, IPO13, ARHGEF28, ATP2A1, SORBS2, AD API, TLE3, C11ORF54, CD58, MOG, DPYS15, HNRNPL, PDIA3, PLXNB3, HUNK, HEY1, MYLPF, SCUBE3, SORBS2, ATP2A1, MFI2, BAIAP2, AD API, RAB11FIP1, MARCKSL1, MOG, IPO13, HUNK, ARHGEF28, NTN1, GPD1, GPT, CD58, HNRNPL, PDIA3, DPYS15, TLE3, C11ORF54, PLXNB3, HEY1, IFI27L2, ARHGAP6, SPON2, SCUBE3, MYLPF, LFNG, HSD3B7, TMEM200B, ABAT, KCTD12, GSTM3, TNNI3, SEMA3E, HES1, UCP2, GALNT15, ADPRHL1, MARCKSL1, RAB11FIP1, ANO8, NTN1, SKAP2, GPT, COX7A2, DKK1, GPD1, BAIAP2, RABEPK, SHD, CEMIP, XYLT1, CPAMD8, PSMB8, FBP1, DLL1, MFI2, TLCD1, IPO13, ANKRD24, GALNT3, ARHGEF28, BCL2L13, THRAP3, SCARA5, MTTP, RANGRF,ATP2A1, WDR83, S0RBS2, ASL, PSMB10, SLC12A8, TM7SF2, AD API, ANXA3, LAMA3, TLE3, FREM2, FAM60A, C11ORF54, MYO16, CD58, ZEB2, STAC3, HYAL2, EMD, CDH2, CRAT, MEI, PLA2G6, LGALS9, DOK7, MOG, HIST1H1E, FRAT2, SLC35D1, BAG2, HNRNPL, C14ORF159, SLC45A3, FMN2, STAC2, TTC28, SLC38A5, PTPRE, LSS, AMOTL2, CACNA1H, GPC5, SLC9A3R1, TPGS1, ARPP21, PLEKHG1, TUBA1A, EIF2AK2, MURC, JPH1, PPP2R3B, BPGM, ARHGAP8, TPCN2, PDIA3, ARSI, IER2, PLXNB3, SPG20, TMEM198B, HUNK, HGD, ALAS1, IFI27L2, ANO8, HEY1V MYLPF, UCP2, ABAT, SCUBE3, ANKRD24, ZEB2, ARHGAP6, SORBS2, ATP2A1, ADPRHL1, MFI2, HES1, BAIAP2, TNNI3, HIST1H1E, TMEM200B, AD API, SEMA3E, MURC, ALAS1, RAB11FIP1, TTC28, CRAT, MARCKSL1, IER2, MOG, XYLT1, SLC45A3, HSD3B7, IPO13, HYAL2, HUNK, FBP1, ARHGEF28, EMD, AMOTL2, MYO16, GALNT15, GPD1, TGM1, CPAMD8, THRAP3, LAMA3, C14ORF159, FREM2, STAC2, GSTM3, JPH1, SHD, HGD, GPC5, DOK7, STAC3, BCL2L13, KCTD12, BPGM, TUBA1A, GALNT3, GPT, HNRNPL, DKK1, PLEKHG1, ARHGAP8, CEMIP, WDR83, NTN1, MEI, BAG2, CACNA1H, RABEPK, SLC9A3R1, TPCN2, PDIA3, LGALS9, RANGRF, LSS, PPP2R3B, SPG20, TM7SF2, EIF2AK2, PSMB8, SLC38A5, TLCD1, FRAT2, SKAP2, CDH2, ASL, FMN2, ARPP21, TPGS1, FAM60A, PLA2G6, PSMB10, COX7A2, SCARA5, DLL1, TLE3, LFNG, MTTP, TMEM198B, PLXNB3, SPON2, ANXA3, SLC35D1, C11ORF54, PTPRE, and a combination thereof.

[0024] In some embodiments, the altered expression profile comprises a change to a gene, a transcript, or a protein selected from the group consisting of ABCG2, SI, NDUFS8, ITGA5, CNTD1, PKHD1L1, PLXNB2, CASP10, FN1, ASAP2, IL13RA2, DAAM2, MCTP1, NUGGC, MEGF10, KIAA1324L, CPXM1, PHACTR4, FGF13, FLT1, PRICKLEI, ZEB1, SULF2, NET1, KIFAP3, HDAC9, DOPEY2, MAN2B2, TLE4, GARNL3, PFKP, ANKS1B, ABHD4, GTPBP2, PLXNA3, CREB3, NLRP12, PTPRK, RGN, GLUL, MMP13, CMYA5, CAMTAI, ABCA1, CDH1, EPHA10, DCHS1, OLFML1, SLC12A5, F8, ARHGAP22, LTBP3, PPP1R42, ADH5, REEP1, ADAMTS1, ATF5, ALDH1L1, ADAMTSL3, CSF1R, BSCL2, SLC15A2, CYP3A4, KIAA1644, ABCC6, GARS, ANTXRL, GGT7, P2RY4, IL1B, PRKAG2, TNFAIP3, VASP, FSTL1, KLHL38, SLC47A2, SLC5A5, FKBP14, MAGI2, GTPBP1, EXOC3L1, RAB37, KRT12, SLCO2B1, ADM2, DACT2, CHRD, ROBO3, MMP19, PTK7, PLEKHH1, FERMT1, SRPX2, TOX3, CTSS, MST1R, CCDC108, SEMA6C, AVPR1A, TSC22D4, FSTL3, ITGA2, PTGIS, COLEC12, NLN, FBXO32, CCDC153, DOCKIO, CYSTM1, FAM214A, CAND2, ARHGEF25, PTPLAD2, PAMR1, ULK2, PRODH, KRT8, TRIM55, KIAA1522, OPLAH, PREXI, LRP2,TBC1D2, INVS, ADAMTS12, MDM2, CSRNP1, RTP4, MED13L, NFKBIA, RGS12, LMNA, RIN1, TCN2, PDE7B, COL23A1, KIAA0141, AATK, IL1RAP, MXRA8, ZMIZ1, TMTC2, ISG15, MAP6, ACSL3, MKL2, ATXN1, WDFY2, CAPN2, ERRFI1, FARP1, HFE2, ZC3H12D, UAP1L1, RNF165, MPP5, SAT1, HBP1, AMPD2, HOMEZ, B3GNT2, STEAP4, PCDHAC2, COL4A3BP, TNS3, RNF169, AEBP1, TFE3, TTYH1, NEIL1, KIAA1033, MMP14, ACSL4, KLHL40, LPIN1, FGD1, XPC,TNFAIP2, CCDC92, DAB2, MTMR11, ZFYVE28, PC, ADIPOR2, MYODI, ZBTB33, METRNL, TBC1D2B, MFAP5, SCD, PPP1R3C, VPS4B, QPCT,CTSH, ARHGAP24, WDFY4, ROR2, ATP6V1B2, CTSZ, CXADR, MFSD2A, AVIL, XKRX, CHRNG, TIFA, TMCC3, SEMA4B, GDF10, PARD3, MAN2B1, PNPLA6, COL15A1, VPS41, TBC1D26, GHDC, HEY1, SCUBE3, MYLPF, MARCKSL1, RAB11FIP1, NTN1, GPT, GPD1, BAIAP2, MFI2, IPO13, ARHGEF28, ATP2A1, SORBS2, AD API, TLE3, C11ORF54, CD58, MOG, DPYS15, HNRNPL, PDIA3, PLXNB3, HUNK, HEY1, IFI27L2, ARHGAP6, SPON2, LFNG, HSD3B7, TMEM200B, ABAT, KCTD12, GSTM3, TNNI3, SEMA3E, HES1, UCP2, GALNT15, ADPRHL1, ANO8, SKAP2, COX7A2, DKK1, RABEPK, SHD, CEMIP, XYLT1, CPAMD8, PSMB8, FBP1, DLL1, TLCD1, ANKRD24, GALNT3, BCL2L13, THRAP3, SCARA5, MTTP, RANGRF, WDR83, ASL, PSMB10, SLC12A8, TM7SF2, ANXA3, LAMA3, FREM2, FAM60A, MYO16, ZEB2, STAC3, HYAL2, EMD, CDH2, CRAT, MEI, PLA2G6, LGALS9, DOK7, HIST1H1E, FRAT2, SLC35D1, BAG2, C14ORF159, SLC45A3, FMN2, STAC2, TTC28, SLC38A5, PTPRE, LSS, AMOTL2, CACNA1H, GPC5, SLC9A3R1, TPGS1, ARPP21, PLEKHG1, TUBA1A, EIF2AK2, MURC, JPH1, PPP2R3B, BPGM, ARHGAP8, TPCN2, ARSI, IER2, SPG20, TMEM198B, HGD, ALAS1, TGM1, and a combination thereof.

[0025] In some embodiments, the altered cell line composition comprises a gene, a transcript, or a protein selected from the group consisting of ABCG2, SI, NDUFS8, ITGA5, CNTD1, PKHD1L1, PLXNB2, CASP10, FN1, ASAP2, IL13RA2, DAAM2, MCTP1, NUGGC, MEGF10, KIAA1324L, CPXM1, PHACTR4, FGF13, FLT1, PRICKLEI, ZEB1, SULF2, NET1, KIFAP3, HDAC9, DOPEY2, MAN2B2, TLE4, GARNL3, PFKP, ANKS1B, ABHD4, GTPBP2, PLXNA3, CREB3, NLRP12, PTPRK, RGN, and a combination thereof.

[0026] In some embodiments, the altered gene expression profile comprises a change to a gene, a transcript, or a protein selected from the group consisting of ABCG2, SI, NDUFS8, ITGA5, CNTD1, PKHD1L1, PLXNB2, CASP10, FN1, ASAP2, IL13RA2, DAAM2, MCTP1, NUGGC, MEGF10, KIAA1324L, CPXM1, PHACTR4, FGF13, FLT1, PRICKLEI, ZEB1, SULF2, NET1, KIFAP3, HDAC9, DOPEY2, MAN2B2, TLE4, GARNL3, PFKP,ANKS1B, ABHD4, GTPBP2, PLXNA3, CREB3, NLRP12, PTPRK, RGN, GLUL, and a combination thereof. In certain embodiments, the change to the selected gene, transcript, or protein comprises a genetic variant comprising a deleterious effect on the resulting protein, compared to an effect of a non-variant gene of a corresponding or reference non-altered cell line or a reference genome. In certain embodiments, the change to the selected gene, transcript, or protein comprises a genetic variant comprising a frameshift, a nonsense, a stop codon, or a loss of function mutation. In certain embodiments, the deleterious effect comprises protein truncation, loss of protein function, and / or triggering of nonsense-mediated protein decay. In certain embodiments, the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is upregulated by a change of 0.5 to about 14 log fold, about 0.5 to about 12 log fold, 0.5 to about 10 log fold, about 0.5 to about 8 log fold, about 0.5 to about 6 log fold, about 0.5 to about 4 log fold, or about 0.5 to about 2 log fold, each inclusive, compared to a reference expression level of the selected gene. In certain embodiments, the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is upregulated by a change of about 1.0 log fold, about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, 7.0 log fold, about 7.5 log fold, about 8.0 log fold, about 8.5 log fold, about 9.0 log fold, about 9.5 log fold, or about 10.0 log fold, compared to a reference expression level of the selected gene.

[0027] In some embodiments, the altered cell line composition comprises a gene, a transcript, or a protein selected from the group consisting of GLUL, ABCG2, SI, MMP13, CMYA5, CAMTAI, ABCA1, CDH1, NDULS8, EPHA10, DCHS1, OLEML1, ITGA5, SLC12A5, E8, CNTD1, PKHD1L1, ARHGAP22, LTBP3, PPP1R42, ADH5, REEP1, ADAMTS1, ATE5, ALDH1L1, ADAMTSL3, PLXNB2, CASP10, CSL1R, BSCL2, SLC15A2, CYP3A4, EN1, KIAA1644, ABCC6, GARS, ANTXRL, ASAP2, GGT7, GARS, P2RY4, ABCA1, IL1B, PRKAG2, TNEAIP3, VASP, ESTL1, IL13RA2, KLHL38, SLC47A2, SLC5A5, EKBP14, MAGI2, GTPBP1, DAAM2, EXOC3L1, RAB37, KRT12, SLCO2B1, ADM2, MCTP1, DACT2, NUGGC, CHRD, ROBO3, MMP19, PTK7, PLEKHH1, MEGE10, EERMT1, SRPX2, TOX3, CTSS, MST1R, CCDC108, SEMA6C, AVPR1A, TSC22D4, ESTL3, ITGA2, PTGIS, COLEC12, KIAA1324L, NLN, LBXO32, CCDC153, CPXM1, PHACTR4, EGE13, DOCK10, CYSTM1, EAM214A, CAND2, ARHGEE25, PTPLAD2, PAMR1, ULK2, PRODH, KRT8, TRIM55, KIAA1522, OPLAH, PREXI, LRP2, TBC1D2, INVS, ELT1, PRICKLEI, ADAMTS12, MDM2, CSRNP1, RTP4,MED13L, NFKBIA, RGS12, LMNA, RIN1, TCN2, PDE7B, COL23A1, KIAA0141, ANTXRL, AATK, ZEB1, IL1RAP, COL23A1, SULF2, MXRA8, ZMIZ1, TMTC2, KIFAP3, ISG15, MAP6, HDAC9, ACSL3, D0PEY2, MAN2B2, GARNL3, MKL2, ATXN1, WDFY2, CAPN2, ERRFI1, FARP1, HFE2, ZC3H12D, PFKP, ANKS1B, UAP1L1, ABHD4, RNF165, MPP5, SAT1, HBP1, AMPD2, HOMEZ, B3GNT2, GTPBP2, STEAP4, PCDHAC2, COL4A3BP, TNS3, RNF169, AEBP1, TFE3, TTYH1, NEIL1, KIAA1033, MMP14, ACSL4, KLHL40, LPIN1, FGD1, XPC, PLXNA3, TNFAIP2, CCDC92, DAB2, MTMR11, ZFYVE28, PC, ADIPOR2, MYODI, ZBTB33, METRNL, TBC1D2B, MFAP5, SCD, PPP1R3C, VPS4B, QPCT, METRNL, CTSH, CREB3, ARHGAP24, WDFY4, ROR2, ATP6V1B2, CTSZ, CXADR, MFSD2A, AVIL, XKRX, NLRP12, PTPRK, CHRNG, TIFA, TMCC3, SEMA4B, GDF10, PARD3, RGN, MAN2B1, PNPLA6, COL15A1, VPS41, TBC1D26, GHDC, ATHL1, NUGGC, TBC1D26, FSTL3, PNPLA6, XKRX, LTBP3, MFAP5, ABCC6, CSF1R, FARP1, SRPX2, LRP2, AATK, KRT12, MCTP1, CCDC153, SLC5A5, KRT8, PAMR1, FN1, and a combination thereof.

[0028] In some embodiments, the altered expression profile comprises a change to a gene, a transcript, or a protein selected from the group consisting of GLUL, ABCG2, SI, MMP13, CMYA5, CAMTAI, ABCA1, CDH1, NDUFS8, EPHA10, DCHS1, OLFML1, ITGA5, SLC12A5, F8, CNTD1, PKHD1L1, ARHGAP22, LTBP3, PPP1R42, ADH5, REEP1, ADAMTS1, ATF5, ALDH1L1, ADAMTSL3, PLXNB2, CASP10, CSF1R, BSCL2, SLC15A2, CYP3A4, FN1, KIAA1644, ABCC6, GARS, ANTXRL, ASAP2, GGT7, GARS, P2RY4, ABCA1, IL1B, PRKAG2, TNFAIP3, VASP, FSTL1, IL13RA2, KLHL38, SLC47A2, SLC5A5, FKBP14, MAGI2, GTPBP1, DAAM2, EXOC3L1, RAB37, KRT12, SLCO2B1, ADM2, MCTP1, DACT2, NUGGC, CHRD, ROBO3, MMP19, PTK7, PLEKHH1, MEGF10, FERMT1, SRPX2, TOX3, CTSS, MST1R, CCDC108, SEMA6C, AVPR1A, TSC22D4, FSTL3, ITGA2, PTGIS, COLEC12, KIAA1324L, NLN, FBXO32, CCDC153, CPXM1, PHACTR4, FGF13, DOCKIO, CYSTM1, FAM214A, CAND2, ARHGEF25, PTPLAD2, PAMR1, ULK2, PRODH, KRT8, TRIM55, KIAA1522, OPLAH, PREXI, LRP2, TBC1D2, INVS, FLT1, PRICKLEI, ADAMTS12, MDM2, CSRNP1, RTP4, MED13L, NFKBIA, RGS12, LMNA, RIN1, TCN2, PDE7B, COL23A1, KIAA0141, ANTXRL, AATK, ZEB1, IL1RAP, COL23A1, SULF2, MXRA8, ZMIZ1, TMTC2, KIFAP3, ISG15, MAP6, HDAC9, ACSL3, DOPEY2, MAN2B2, GARNL3, MKL2, ATXN1, WDFY2, CAPN2, ERRFI1, FARP1, HFE2, ZC3H12D, PFKP, ANKS1B, UAP1L1, ABHD4, RNF165, MPP5, SAT1, HBP1, AMPD2, HOMEZ, B3GNT2, GTPBP2, STEAP4, PCDHAC2, COL4A3BP, TNS3, RNF169, AEBP1, TFE3, TTYH1, NEIL1, KIAA1033,MMP14, ACSL4, KLHL40, LPIN1, FGD1, XPC, PLXNA3, TNFAIP2, CCDC92, DAB2, MTMR11, ZFYVE28, PC, ADIPOR2, MYODI, ZBTB33, METRNL, TBC1D2B, MFAP5, SCD, PPP1R3C, VPS4B, QPCT, METRNL, CTSH, CREB3, ARHGAP24, WDFY4, ROR2, ATP6V1B2, CTSZ, CXADR, MFSD2A, AVIL, XKRX, NLRP12, PTPRK, CHRNG, TIFA, TMCC3, SEMA4B, GDF10, PARD3, RGN, MAN2B1, PNPLA6, COL15A1, VPS41, TBC1D26, GHDC, ATHL1, and a combination thereof. In certain embodiments, the change to the selected gene, transcript, or protein comprises a genetic variant comprising a non- deleterious effect on the resulting protein, compared an effect of a non-variant gene of a corresponding or reference non-altered cell line or a reference genome. In certain embodiments, the change to the selected gene, transcript, or protein comprises a genetic variant comprising an intragenic or an intron variant. In specific embodiments, the non- deleterious effect comprises an alteration or a change in effectiveness of the resulting protein. In particular embodiments, the effectiveness of the resulting protein is decreased. In particular embodiments, the effectiveness of the resulting protein is increased. In certain embodiments, the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is upregulated by a change of about 0.5 to about 14 log fold, about 0.5 to about 12 log fold, 0.5 to about 10 log fold, about 0.5 to about 8 log fold, about 0.5 to about 6 log fold, about 0.5 to about 4 log fold, or about 0.5 to about 2 log fold, each inclusive, compared to a reference expression level of the selected gene. In certain embodiments, the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is upregulated by a change of about 1.0 log fold, about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, 7.0 log fold, about 7.5 log fold, about 8.0 log fold, about 8.5 log fold, about 9.0 log fold, about 9.5 log fold, or about 10.0 log fold, compared to a reference expression level of the selected gene.

[0029] In some embodiments, the altered cell line composition comprises a gene, a transcript, or a protein selected from the group consisting of HEY1, SCUBE3, MYLPF, MARCKSL1, RAB11FIP1, NTN1, GPT, GPD1, BAIAP2, MFI2, IPO13, ARHGEF28, ATP2A1, SORBS2, AD API, TLE3, C11ORF54, CD58, MOG, DPYS15, HNRNPL, PDIA3, PLXNB3, HUNK, HEY1, MYLPF, SCUBE3, SORBS2, ATP2A1, MFI2, BAIAP2, AD API, RAB11FIP1, MARCKSL1, MOG, IPO13, HUNK, ARHGEF28, NTN1, GPD1, GPT, CD58, HNRNPL, PDIA3, DPYS15, TLE3, C11ORF54, PLXNB3, and a combination thereof.

[0030] In some embodiments, the altered expression profile comprises a change to a gene, a transcript, or a protein selected from the group consisting of HEY1, SCUBE3, MYLPF, MARCKSL1, RAB11FIP1, NTN1, GPT, GPD1, BAIAP2, MFI2, IPO13, ARHGEF28, ATP2A1, SORBS2, AD API, TLE3, C11ORF54, CD58, MOG, DPYS15, HNRNPL, PDIA3, PLXNB3, HUNK, and a combination thereof. In certain embodiments, the change to the selected gene, transcript, or protein comprises a genetic variant comprising a deleterious effect on the resulting protein, compared to an effect of a non-variant gene of a corresponding or reference non-altered cell line or a reference genome. In certain embodiments, the change to the selected gene, transcript, or protein comprises a genetic variant comprising a frameshift, a nonsense, a stop codon, or a loss of function mutation. In certain embodiments, the deleterious effect comprises protein truncation, loss of protein function, and / or triggering of nonsense-mediated protein decay. In certain embodiments, the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is downregulated by a change of 0.5 to about 14 log fold, about 0.5 to about 12 log fold, 0.5 to about 10 log fold, about 0.5 to about 8 log fold, about 0.5 to about 6 log fold, about 0.5 to about 4 log fold, or about 0.5 to about 2 log fold, each inclusive, compared to a reference expression level of the selected gene. In certain embodiments, the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is downregulated by a change of about 1.0 log fold, about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, 7.0 log fold, about 7.5 log fold, about 8.0 log fold, about 8.5 log fold, about 9.0 log fold, about 9.5 log fold, or about 10.0 log fold, compared to a reference expression level of the selected gene.

[0031] In some embodiments, the altered cell line composition comprises a gene, a transcript, or a protein selected from the group consisting of HEY1, IFI27L2, ARHGAP6, SPON2, SCUBE3, MYLPF, LFNG, HSD3B7, TMEM200B, ABAT, KCTD12, GSTM3, TNNI3, SEMA3E, HES1, UCP2, GALNT15, ADPRHL1, MARCKSL1, RAB11FIP1, ANO8, NTN1, SKAP2, GPT, COX7A2, DKK1, GPD1, BAIAP2, RABEPK, SHD, CEMIP, XYLT1, CPAMD8, PSMB8, FBP1, DLL1, MFI2, TLCD1, IPO13, ANKRD24, GALNT3, ARHGEF28, BCL2L13, THRAP3, SCARA5, MTTP, RANGRF, ATP2A1, WDR83, SORBS2, ASL, PSMB10, SLC12A8, TM7SF2, AD API, ANXA3, LAMA3, TLE3, FREM2, FAM60A, C11ORF54, MY016, CD58, ZEB2, STAC3, HYAL2, EMD, CDH2, CRAT, MEI, PLA2G6, LGALS9, D0K7, MOG, HIST1H1E, FRAT2, SLC35D1, BAG2, HNRNPL,C14ORF159, SLC45A3, FMN2, STAC2, TTC28, SLC38A5, PTPRE, LSS, AM0TL2, CACNA1H, GPC5, SLC9A3R1, TPGS1, ARPP21, PLEKHG1, TUBA1A, EIF2AK2, MURC, JPH1, PPP2R3B, BPGM, ARHGAP8, TPCN2, PDIA3, ARSI, IER2, PLXNB3, SPG20, TMEM198B, HUNK, HGD, ALAS1, IFI27L2, AN08, HEY1V MYLPF, UCP2, ABAT, SCUBE3, ANKRD24, ZEB2, ARHGAP6, S0RBS2, ATP2A1, ADPRHL1, MFI2, HES1, BAIAP2, TNNI3, HIST1H1E, TMEM200B, AD API, SEMA3E, MURC, ALAS1, RAB11FIP1, TTC28, CRAT, MARCKSL1, IER2, MOG, XYLT1, SLC45A3, HSD3B7, IPO13, HYAL2, HUNK, FBP1, ARHGEF28, EMD, AMOTL2, MYO16, GALNT15, GPD1, TGM1, CPAMD8, THRAP3, LAMA3, C14ORF159, FREM2, STAC2, GSTM3, JPH1, SHD, HGD, GPC5, DOK7, STAC3, BCL2L13, KCTD12, BPGM, TUBA1A, GALNT3, GPT, HNRNPL, DKK1, PLEKHG1, ARHGAP8, CEMIP, WDR83, NTN1, MEI, BAG2, CACNA1H, RABEPK, SLC9A3R1, TPCN2, PDIA3, LGALS9, RANGRF, LSS, PPP2R3B, SPG20, TM7SF2, EIF2AK2, PSMB8, SLC38A5, TLCD1, FRAT2, SKAP2, CDH2, ASL, FMN2, ARPP21, TPGS1, FAM60A, PLA2G6, PSMB10, COX7A2, SCARA5, DLL1, TLE3, LFNG, MTTP, TMEM198B, PLXNB3, SPON2, ANXA3, SLC35D1, C11ORF54, PTPRE, and a combination thereof.

[0032] In certain embodiments, the altered expression profile comprises a change to a gene, a transcript, or a protein selected from the group consisting of HEY1, IFI27L2, ARHGAP6, SPON2, SCUBE3, MYLPF, LFNG, HSD3B7, TMEM200B, ABAT, KCTD12, GSTM3, TNNI3, SEMA3E, HES1, UCP2, GALNT15, ADPRHL1, MARCKSL1, RAB11FIP1, ANO8, NTN1, SKAP2, GPT, COX7A2, DKK1, GPD1, BAIAP2, RABEPK, SHD, CEMIP, XYLT1, CPAMD8, PSMB8, FBP1, DLL1, MFI2, TLCD1, IPO13, ANKRD24, GALNT3, ARHGEF28, BCL2L13, THRAP3, SCARA5, MTTP, RANGRF, ATP2A1, WDR83, SORBS2, ASL, PSMB10, SLC12A8, TM7SF2, AD API, ANXA3, LAMA3, TLE3, FREM2, FAM60A, C11ORF54, MY016, CD58, ZEB2, STAC3, HYAL2, EMD, CDH2, CRAT, MEI, PLA2G6, LGALS9, DOK7, MOG, HIST1H1E, FRAT2, SLC35D1, BAG2, HNRNPL, C14ORF159, SLC45A3, FMN2, STAC2, TTC28, SLC38A5, PTPRE, LSS, AMOTL2, CACNA1H, GPC5, SLC9A3R1, TPGS1, ARPP21, PLEKHG1, TUBA1A, EIF2AK2, MURC, JPH1, PPP2R3B, BPGM, ARHGAP8, TPCN2, PDIA3, ARSI, IER2, PLXNB3, SPG20, TMEM198B, HUNK, HGD, ALAS1, TGM1, and a combination thereof. In certain embodiments, the change to the selected gene, transcript, or protein comprises a genetic variant comprising a non-deleterious effect on the resulting protein, compared an effect of a non-variant gene of a corresponding or reference non-altered cell line or a reference genome. In certain embodiments, the change to the selected gene, transcript,or protein comprises a genetic variant comprising an intragenic or an intron variant. In specific embodiments, the non-deleterious effect comprises an alteration or a change in effectiveness of the resulting protein. In particular embodiments, the effectiveness of the resulting protein is decreased. In particular embodiments, the effectiveness of the resulting protein is increased. In certain embodiments, the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is downregulated by a change of about 0.5 to about 14 log fold, about 0.5 to about 12 log fold, 0.5 to about 10 log fold, about 0.5 to about 8 log fold, about 0.5 to about 6 log fold, about 0.5 to about 4 log fold, or about 0.5 to about 2 log fold, each inclusive, compared to a reference expression level of the selected gene. In certain embodiments, the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is downregulated by a change of about 1.0 log fold, about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, 7.0 log fold, about 7.5 log fold, about 8.0 log fold, about 8.5 log fold, about 9.0 log fold, about 9.5 log fold, or about 10.0 log fold, compared to a reference expression level of the selected gene.

[0033] In some embodiments, the altered cell line composition comprises a cell line that has been altered with mutagenesis, chemical mutagens, physical mutagens, electromagnetic radiation, particle radiation, CRISPR, transfection, viruses, non-integrative nucleic acid molecules, or a combination thereof. In some embodiments, the chemical mutagen is an alkylating agent or an azide. In some embodiments, the alkylating agent is selected from the group consisting of N-etyl-N-nitrosourea (ENU), ethyl methanesulfonate (EMS), and combinations thereof.

[0034] In some embodiments, the altered cell line composition has been altered with electromagnetic radiation selected from the group consisting of gamma rays, x-rays, UV light, and combinations thereof.

[0035] In some embodiments, the altered cell line composition has been altered with particle radiation selected from the group consisting of fast neutrons, thermal neutrons, beta particles, alpha particles, and combinations thereof.

[0036] In some embodiments, the altered cell line has been altered with mutagenesis, chemical mutagens, physical mutagens, electromagnetic radiation, particle radiation, CRISPR, transfection, viruses, non-integrative nucleic acid molecules, or a combination thereof. In particular embodiments, In some embodiments, wherein the altered cell line has been altered with alkylating agents and azides. In particular embodiments, the altered cellline has been altered with alkylating agents selected from the group consisting of N-ethyl-N- nitrosourea (ENU), ethyl methanesulfonate (EMS), and a combination thereof. In some embodiments, the altered cell line has been altered with electromagnetic radiation selected from the group consisting of gamma rays, x-rays, UV light, and a combination thereof. In some embodiments, the altered cell line has been altered with particle radiation selected from the group consisting of fast neutrons, thermal neutrons, beta particles, alpha particles, and a combination thereof.

[0037] In some embodiments, the altered cell line, the non-altered cell line, and / or the reference genome is derived an aquatic species comprising at least one species selected from the group consisting of bass, flounder, hake, scup, smelt, rainbow trout, hardshell clam, blue crab, peekytoe crab, spanner crab, cuttlefish, Eastern oyster, Pacific oyster, anchovy, herring, lingcod, moi, orange roughy, Atlantic Ocean perch, Lake Victoria perch, yellow perch, European oyster, Dover sole, sturgeon, tilefish, wahoo, yellowtail, sea urchin, Atlantic mackerel, sardines, black sea bass, European sea bass, hybrid striped bass, bream, cod, drum, haddock, hoki, Alaska pollock, rockfish, pink salmon, snapper, tilapia, turbot, walleye, lake whitefish, wolffish, hardshell clam, surf clam, cockle, Jonah crab, snow crab, crayfish, bay scallop, Chinese white shrimp, sablefish, Atlantic salmon, coho salmon, skate, dungeness crab, king crab, blue mussel, greenshell mussel, pink shrimp, Escolar, chinook salmon, chum salmon, American shad, Arctic char, carp, catfish, dory, grouper, halibut, monkfish, pompano, abalone, conch, stone crab, American lobster, spiny lobster, octopus, black tiger shrimp, freshwater shrimp, gulf shrimp, Pacific white shrimp, squid, barramundi, cusk, dogfish, kingklip, mahi-mahi, opah, mako shark, swordfish, albacore tuna, yellowfin tuna, geoduck clam, squat lobster, sea scallop, rock shrimp, barracuda, Chilean sea bass, cobia, croaker, eel, blue marlin, mullet, sockeye salmon, Bluefin tuna, shrimp, crabs, lobster, and echinoderms (e.g. sea cucumbers and sea urchins).

[0038] In some embodiments, the altered cell line, the non-altered cell line, and / or the reference genome is derived from an aquatic species comprising at least one species selected from the group consisting of Bluefin tuna (Thunnus orientalis, Thunnus maccoyii, and Thunnus thynnus), yellowfin tuna (Thunnus albacares), yellowtail (e.g., Seriola lalandi), mahi-mahi (Coryphaena hippurus), red snapper (Lutjanus campechanus), cod (e.g., Gadus morhua, Gadus Macrocephalus, Gadus ogac), flounder, halibut, herring, mackeral, pompano, salmon (Salmo salar), sea bass, Patagonian toothfish (Dissostichus eleginoides), squid, clams, lobster, crabs, scallops, shrimp, eel, bass (e.g., Micropterus salmoides), bluegill (Lepomis macrochirus), rainbow trout (Oncorhynchus mykiss), tilapia (Oreochromismassambicus), and carp (e.g., Hypophthalmichthys molitrix). In specific embodiments, , the altered cell line, the non-altered cell line, and / or the reference genome is derived from an aquatic species comprising at least one species selected from the group consisting of the eight species of tunas in the genus Thunnus. These include the northern Bluefin tuna (T. thynnus), albacore (T. alalunga), yellowfin tuna (T. albacares), southern Bluefin tuna (T. thynnus maccoyii), bigeye tuna (T. obesus), blackfin tuna (T. allanlicus), Pacific Bluefin tuna (Thunnus orientalis), and longtail tuna (T. longgol). In particular embodiments, the altered cell line, the non-altered cell line, and / or the reference genome is derived from Thunnus orientalis.

[0039] In some embodiments, the altered cell line composition is derived from an aquatic species comprising at least one species selected from the group consisting of Bluefin tuna (Thunnus orientalis, Thunnus maccoyii, and Thunnus thynnus), yellowfin tuna (Thunnus albacares), yellowtail (e.g., Seriola lalandi), mahi-mahi (Coryphaena hippurus), red snapper (Lutjanus campechanus), cod (e.g., Gadus morhua, Gadus Macrocephalus, Gadus ogac), flounder, halibut, herring, mackeral, pompano, salmon (Salmo salar), sea bass, Patagonian toothfish (Dissostichus eleginoides), squid, clams, lobster, crabs, scallops, shrimp, eel, bass (e.g., Micropterus salmoides), bluegill (Lepomis macrochirus), rainbow trout (Oncorhynchus mykiss), tilapia (Oreochromis massambicus), and carp (e.g., Hypophthalmichthys molitrix). In a preferred embodiment, the altered cell line composition is derived from Thunnus orientalis.

[0040] In another embodiment the altered cell line composition is derived from an aquatic species comprising at least one species selected from the group consisting of the eight species of tunas in the genus Thunnus. These include the northern Bluefin tuna (T. thynnus), albacore (T. alalunga), yellowfin tuna (T. albacares), southern Bluefin tuna (T. thynnus maccoyii), bigeye tuna (T. obesus), blackfin tuna (T. atlanticus), Pacific Bluefin tuna (Thunnus orientalis), and longtail tuna (T. tonggol).

[0041] In addition to the altered cell line composition being derived from the genus Thunnus, particularly Bluefin tuna cells, cells from a wide variety of fish species can be used. Such species include but are not limited to bass, flounder, hake, scup, smelt, rainbow trout, hardshell clam, blue crab, peekytoe crab, spanner crab, cuttlefish, Eastern oyster, Pacific oyster, anchovy, herring, lingcod, moi, orange roughy, Atlantic Ocean perch, Lake Victoria perch, yellow perch, European oyster, Dover sole, sturgeon, tilefish, wahoo, yellowtail, sea urchin, Atlantic mackerel, sardines, black sea bass, European sea bass, hybrid striped bass, bream, cod, drum, haddock, hoki, Alaska pollock, rockfish, pink salmon, snapper, tilapia, turbot, walleye, lake whitefish, wolffish, hardshell clam, surf clam, cockle, Jonah crab, snowcrab, crayfish, bay scallop, Chinese white shrimp, sablefish, Atlantic salmon, coho salmon, skate, dungeness crab, king crab, blue mussel, greenshell mussel, pink shrimp, Escolar, chinook salmon, chum salmon, American shad, Arctic char, carp, catfish, dory, grouper, halibut, monkfish, pompano, abalone, conch, stone crab, American lobster, spiny lobster, octopus, black tiger shrimp, freshwater shrimp, gulf shrimp, Pacific white shrimp, squid, barramundi, cusk, dogfish, kingklip, mahi-mahi, opah, mako shark, swordfish, albacore tuna, yellowfin tuna, geoduck clam, squat lobster, sea scallop, rock shrimp, barracuda, Chilean sea bass, cobia, croaker, eel, blue marlin, mullet, sockeye salmon, Bluefin tuna, shrimp, crabs, lobster, and echinoderms (e.g. sea cucumbers and sea urchins).

[0042] Provided herein are methods for generating an altered cell line, the method comprising (a) providing an adherent cell line or derivative thereof; and (b) subjecting the adherent cell line or derivative thereof to a process sufficient to generate an altered cell line comprising an altered expression profile that is different than an expression profile of a corresponding non-altered cell line. Also provided herein are methods for (a) providing an adherent cell line or derivative thereof; and (b) subjecting the adherent cell line or derivative thereof to a process sufficient to generate an altered cell line comprising an altered expression profile comprising: (1) an altered gene expression profile that is different than a gene expression profile of the adherent cell line or derivative used in (a) and / or a reference nonaltered cell line; and / or (2) an altered phenotypic profile that is different than a phenotypic profile of the adherent cell line or derivative used in (a) and / or a reference non-altered cell line.

[0043] In certain embodiments, the altered phenotypic profile comprises of improved viability and stabilized growth rates in (1) non-adherent, suspension cell culture, (2) serum- free media cell culture, and / or (3) animal component-free media culture. In some embodiments, the altered cell line is a suspension cell line. In some embodiments, the altered cell line is an altered adherent cell line. In some embodiments, the subjecting in step (b) is performed in vitro.

[0044] In some embodiments, the present disclosure provides a method for generating an altered cell line, the method comprising (a) providing an adherent cell line or derivative thereof; and (b) subjecting said adherent cell line or derivative thereof to a process sufficient to generate an altered expression profile that is different than an expression profile of a corresponding non-altered cell line. In some embodiments, the method generates an altered cell line that is a suspension cell line. In some embodiments, the method generates an altered cell line that is an adherent cell line.

[0045] In some embodiments, step (b) of the method is performed in vitro.

[0046] In some embodiments, the adherent cell line or derivative, the generated altered cell line, and / or the non-altered cell line is derived from an aquatic species. In some embodiments, the adherent cell line or derivative, the generated altered cell line, and / or the non-altered cell line is derived from an aquatic species comprising at least one species selected from the group consisting of bass, flounder, hake, scup, smelt, rainbow trout, hardshell clam, blue crab, peekytoe crab, spanner crab, cuttlefish, Eastern oyster, Pacific oyster, anchovy, herring, lingcod, moi, orange roughy, Atlantic Ocean perch, Lake Victoria perch, yellow perch, European oyster, Dover sole, sturgeon, tilefish, wahoo, yellowtail, sea urchin, Atlantic mackerel, sardines, black sea bass, European sea bass, hybrid striped bass, bream, cod, drum, haddock, hoki, Alaska pollock, rockfish, pink salmon, snapper, tilapia, turbot, walleye, lake whitefish, wolffish, hardshell clam, surf clam, cockle, Jonah crab, snow crab, crayfish, bay scallop, Chinese white shrimp, sablefish, Atlantic salmon, coho salmon, skate, dungeness crab, king crab, blue mussel, greenshell mussel, pink shrimp, Escolar, chinook salmon, chum salmon, American shad, Arctic char, carp, catfish, dory, grouper, halibut, monkfish, pompano, abalone, conch, stone crab, American lobster, spiny lobster, octopus, black tiger shrimp, freshwater shrimp, gulf shrimp, Pacific white shrimp, squid, barramundi, cusk, dogfish, kingklip, mahi-mahi, opah, mako shark, swordfish, albacore tuna, yellowfin tuna, geoduck clam, squat lobster, sea scallop, rock shrimp, barracuda, Chilean sea bass, cobia, croaker, eel, blue marlin, mullet, sockeye salmon, Bluefin tuna, shrimp, crabs, lobster, and echinoderms (e.g. sea cucumbers and sea urchins). In some embodiments, the adherent cell line or derivative, the generated altered cell line, and / or the non-altered cell line is derived from an aquatic species comprising at least one species selected from the group consisting of Bluefin tuna (Thunnus orientalis and Thunnus thynnus), yellowfin tuna (Thunnus albacares), yellowtail (e.g., Seriola lalandi), mahi-mahi (Coryphaena hip pur us). red snapper (Lutjanus campechanus). cod (e.g., Gadus morhua, Gadus Macrocephalus, Gadus ogac), flounder, halibut, herring, mackeral, pompano, salmon (Salmo salar), sea bass, Patagonian toothfish (Dissostichus eleginoides), squid, clams, lobster, crabs, scallops, shrimp, eel, bass (e.g., Micropterus salmoides). bluegill (Lepomis macrochirus), rainbow trout (Oncorhynchus rnykiss), tilapia (Oreochromis massambicus), and carp (e.g., Hypophthalmichthys molitrix). In specific embodiments, the adherent cell line or derivative, the generated altered cell line, and / or the non-altered cell line is derived from an aquatic species comprising at least one species selected from the group consisting of northern Bluefin tuna (T. thynnus), albacore (T. alalunga), yellowfin tuna (T. albacares'), southern Bluefin tuna(T. thynnus maccoyii), bigeye tuna (T. obesus), blackfin tuna (T. atlanticus), Pacific Bluefin tuna (Thunnus orientalis), and longtail tuna (T. tonggol).

[0047] In some embodiments, the method generates an altered cell line that is derived from an aquatic species. In some embodiments, the method generates an altered cell line from an aquatic species comprising at least one species selected from the group consisting of Bluefin tuna (Thunnus orientalis, Thunnus maccoyii, and Thunnus thynnus), yellowfin tuna (Thunnus albacares), yellowtail (e.g., Seriola lalandi), mahi-mahi (Coryphaena hippurus), red snapper (Lutjanus campechanus), cod (e.g., Gadus morhua, Gadus Macrocephalus, Gadus ogac), flounder, halibut, herring, mackeral, pompano, salmon (Salmo salar), sea bass, Patagonian toothfish (Dissostichus eleginoides), squid, clams, lobster, crabs, scallops, shrimp, eel, bass (e.g., Micropterus salmoides), bluegill (Lepomis macrochirus), rainbow trout (Oncorhynchus mykiss), tilapia (Oreochromis massambicus), and carp (e.g., Hypophthalmichthys molitrix). In a preferred embodiment, the species is Thunnus orientalis.

[0048] In another embodiment the method generates an altered cell that is derived from an aquatic species comprising at least one species selected from the group consisting of the eight species of tunas in the genus Thunnus. These include the northern Bluefin tuna (T. thynnus), albacore (T. alalunga), yellowfin tuna (T. albacares), southern Bluefin tuna (T. thynnus maccoyii), bigeye tuna (T. obesus), blackfin tuna (T. atlanticus), Pacific Bluefin tuna (Thunnus orientalis), and longtail tuna (T. tonggol).

[0049] In addition to altered cells derived from the genus Thunnus, particularly Bluefin tuna cells, cells from a wide variety of fish species can be used for the method of generation. Such species include but are not limited to bass, flounder, hake, scup, smelt, rainbow trout, hardshell clam, blue crab, peekytoe crab, spanner crab, cuttlefish, Eastern oyster, Pacific oyster, anchovy, herring, lingcod, moi, orange roughy, Atlantic Ocean perch, Lake Victoria perch, yellow perch, European oyster, Dover sole, sturgeon, tilefish, wahoo, yellowtail, sea urchin, Atlantic mackerel, sardines, black sea bass, European sea bass, hybrid striped bass, bream, cod, drum, haddock, hoki, Alaska pollock, rockfish, pink salmon, snapper, tilapia, turbot, walleye, lake whitefish, wolffish, hardshell clam, surf clam, cockle, Jonah crab, snow crab, crayfish, bay scallop, Chinese white shrimp, sablefish, Atlantic salmon, coho salmon, skate, dungeness crab, king crab, blue mussel, greenshell mussel, pink shrimp, Escolar, chinook salmon, chum salmon, American shad, Arctic char, carp, catfish, dory, grouper, halibut, monkfish, pompano, abalone, conch, stone crab, American lobster, spiny lobster, octopus, black tiger shrimp, freshwater shrimp, gulf shrimp, Pacific white shrimp, squid, barramundi, cusk, dogfish, kingklip, mahi-mahi, opah, mako shark, swordfish, albacore tuna,yellowfin tuna, geoduck clam, squat lobster, sea scallop, rock shrimp, barracuda, Chilean sea bass, cobia, croaker, eel, blue marlin, mullet, sockeye salmon, Bluefin tuna, shrimp, crabs, lobster, and echinoderms (e.g. sea cucumbers and sea urchins).

[0050] In some embodiments, the process sufficient to generate the altered cell line comprises contacting the adherent cell line or derivative thereof with a chemical mutagen, a physical mutagen, electromagnetic radiation, particle radiation, a virus, non-integrative nucleic acid molecules, or a combination thereof. In some embodiments, the process sufficient to generate the altered cell line comprises contacting the adherent cell line or derivative thereof with an heterologous gene including a gene regulating moiety, wherein the gene regulating moiety is configured to regulate and / or modify an expression of a target gene, a target transcript, or a target protein of the adherent cell line or derivative thereof, thereby effecting the altered expression profile of the target gene, the transcript, or the target protein in the altered cell line as compared to the corresponding or reference non-altered cell line.

[0051] In some embodiments, the method for generating an altered cell line comprises contacting the adherent cell line with a chemical mutagen, a physical mutagen, electromagnetic radiation, particle radiation, a virus, non-integrative nucleic acid molecules, or combinations thereof. In some embodiments, the chemical mutagen is selected from a group consisting of alkylating agents, azides, and a combination thereof. In some embodiments, the particle radiation is selected from the group consisting of fast neutrons, thermal neutrons, beta particles, alpha particles, and combinations thereof. In some embodiments, the electromagnetic radiation is selected from the group consisting of gamma ray, x-rays, UV light, and combinations thereof.

[0052] In some embodiments, the method for generating an altered cell line comprises contacting the adherent cell line with a heterologous gene including a gene regulating moiety, wherein said gene regulating moiety is configured to regulate an expression of a target gene, a target transcript, or a target protein of the adherent cell line or derivative thereof, thereby effecting a modified expression profile of the target gene, the transcript, or the target protein in the altered suspension cell line as compared to the corresponding non-altered cell line. In some embodiments, the gene regulating moiety is an endonuclease. In some embodiments, the endonuclease is a clustered regularly interspaced short palindromic repeats (CRISPR)- associated (CAS) endonuclease.

[0053] In some embodiments, the method for generating an altered cell line comprising (a) providing an adherent cell line or derivative thereof; and (b) subjecting said adherent cell line or derivative thereof to a process sufficient to generate an altered expression profile thatis different than an expression profile of a corresponding non-altered cell line comprises an expression profile comprising an upregulated gene expression profile. In some embodiments the expression profile comprises a downregulated gene expression profile.

[0054] In certain embodiments, the altered expression profile comprises an upregulated gene expression profile. In certain embodiments, the altered expression profile comprises a downregulated gene expression profile.

[0055] In some embodiments, the method for generating an altered cell line comprises an altered cell line comprising a gene, a transcript, or a protein selected from the group consisting of ABCG2, SI, NDUFS8, ITGA5, CNTD1, PKHD1L1, PLXNB2, CASP10, FN1, ASAP2, IL13RA2, DAAM2, MCTP1, NUGGC, MEGF10, KIAA1324L, CPXM1, PHACTR4, FGF13, FLT1, PRICKLEI, ZEB1, SULF2, NET1, KIFAP3, HDAC9, DOPEY2, MAN2B2, TLE4, GARNL3, PFKP, ANKS1B, ABHD4, GTPBP2, PLXNA3, CREB3, NLRP12, PTPRK, RGN, GLUL, ABCG2, SI, MMP13, CMYA5, CAMTAI, ABCA1, CDH1, NDUFS8, EPHA10, DCHS1, OLFML1, ITGA5, SLC12A5, F8, CNTD1, PKHD1L1, ARHGAP22, LTBP3, PPP1R42, ADH5, REEP1, ADAMTS1, ATF5, ALDH1L1, ADAMTSL3, PLXNB2, CASP10, CSF1R, BSCL2, SLC15A2, CYP3A4, FN1, KIAA1644, ABCC6, GARS, ANTXRL, ASAP2, GGT7, GARS, P2RY4, ABCA1, IL1B, PRKAG2, TNFAIP3, VASP, FSTL1, IL13RA2, KLHL38, SLC47A2, SLC5A5, FKBP14, MAGI2, GTPBP1, DAAM2, EXOC3L1, RAB37, KRT12, SLCO2B1, ADM2, MCTP1, DACT2, NUGGC, CHRD, ROBO3, MMP19, PTK7, PLEKHH1, MEGF10, FERMT1, SRPX2, TOX3, CTSS, MST1R, CCDC108, SEMA6C, AVPR1A, TSC22D4, FSTL3, ITGA2, PTGIS, COLEC12, KIAA1324L, NLN, FBXO32, CCDC153, CPXM1, PHACTR4, FGF13, DOCK10, CYSTM1, FAM214A, CAND2, ARHGEF25, PTPLAD2, PAMR1, ULK2, PRODH, KRT8, TRIM55, KIAA1522, OPLAH, PREXI, LRP2, TBC1D2, INVS, FLT1, PRICKLEI, ADAMTS12, MDM2, CSRNP1, RTP4, MED13L, NFKBIA, RGS12, LMNA, RIN1, TCN2, PDE7B, COL23A1, KIAA0141, ANTXRL, AATK, ZEB1, IL1RAP, COL23A1, SULF2, MXRA8, ZMIZ1, TMTC2, KIFAP3, ISG15, MAP6, HDAC9, ACSL3, DOPEY2, MAN2B2, GARNL3, MKL2, ATXN1, WDFY2, CAPN2, ERRFI1, FARP1, HFE2, ZC3H12D, PFKP, ANKS1B, UAP1L1, ABHD4, RNF165, MPP5, SAT1, HBP1, AMPD2, HOMEZ, B3GNT2, GTPBP2, STEAP4, PCDHAC2, COL4A3BP, TNS3, RNF169, AEBP1, TFE3, TTYH1, NEIL1, KIAA1033, MMP14, ACSL4, KLHL40, LPIN1, FGD1, XPC, PLXNA3, TNFAIP2, CCDC92, DAB2, MTMR11, ZFYVE28, PC, ADIPOR2, MYODI, ZBTB33, METRNL, TBC1D2B, MFAP5, SCD, PPP1R3C, VPS4B, QPCT, METRNL, CTSH, CREB3, ARHGAP24, WDFY4, ROR2, ATP6V1B2, CTSZ, CXADR,MFSD2A, AVIL, XKRX, NLRP12, PTPRK, CHRNG, TIFA, TMCC3, SEMA4B, GDF10, PARD3, RGN, MAN2B1, PNPLA6, COL15A1, VPS41, TBC1D26, GHDC, ATHL1, NUGGC, TBC1D26, FSTL3, PNPLA6, XKRX, LTBP3, MFAP5, ABCC6, CSF1R, FARP1, SRPX2, LRP2, AATK, KRT12, MCTP1, CCDC153, SLC5A5, KRT8, PAMR1, FN1, HEY1, SCUBE3, MYLPF, MARCKSL1, RAB11FIP1, NTN1, GPT, GPD1, BAIAP2, MFI2, IPO13, ARHGEF28, ATP2A1, SORBS2, AD API, TLE3, C11ORF54, CD58, MOG, DPYS15, HNRNPL, PDIA3, PLXNB3, HUNK, HEY1, MYLPF, SCUBE3, SORBS2, ATP2A1, MFI2, BAIAP2, AD API, RAB11FIP1, MARCKSL1, MOG, IPO13, HUNK, ARHGEF28, NTN1, GPD1, GPT, CD58, HNRNPL, PDIA3, DPYS15, TLE3, C11ORF54, PLXNB3, HEY1, IFI27L2, ARHGAP6, SPON2, SCUBE3, MYLPF, LFNG, HSD3B7, TMEM200B, ABAT, KCTD12, GSTM3, TNNI3, SEMA3E, HES1, UCP2, GALNT15, ADPRHL1, MARCKSL1, RAB11FIP1, ANO8, NTN1, SKAP2, GPT, COX7A2, DKK1, GPD1, BAIAP2, RABEPK, SHD, CEMIP, XYLT1, CPAMD8, PSMB8, FBP1, DLL1, MFI2, TLCD1, IPO13, ANKRD24, GALNT3, ARHGEF28, BCL2L13, THRAP3, SCARA5, MTTP, RANGRF, ATP2A1, WDR83, SORBS2, ASL, PSMB10, SLC12A8, TM7SF2, AD API, ANXA3, LAMA3, TLE3, FREM2, FAM60A, C11ORF54, MYO16, CD58, ZEB2, STAC3, HYAL2, EMD, CDH2, CRAT, MEI, PLA2G6, LGALS9, DOK7, MOG, HIST1H1E, FRAT2, SLC35D1, BAG2, HNRNPL, C14ORF159, SLC45A3, FMN2, STAC2, TTC28, SLC38A5, PTPRE, LSS, AMOTL2, CACNA1H, GPC5, SLC9A3R1, TPGS1, ARPP21, PLEKHG1, TUBA1A, EIF2AK2, MURC, JPH1, PPP2R3B, BPGM, ARHGAP8, TPCN2, PDIA3, ARSI, IER2, PLXNB3, SPG20, TMEM198B, HUNK, HGD, ALAS1, IFI27L2, ANO8, HEY1V MYLPF, UCP2, ABAT, SCUBE3, ANKRD24, ZEB2, ARHGAP6, SORBS2, ATP2A1, ADPRHL1, MFI2, HES1, BAIAP2, TNNI3, HIST1H1E, TMEM200B, AD API, SEMA3E, MURC, ALAS1, RAB11FIP1, TTC28, CRAT, MARCKSL1, IER2, MOG, XYLT1, SLC45A3, HSD3B7, IPO13, HYAL2, HUNK, FBP1, ARHGEF28, EMD, AMOTL2, MYO16, GALNT15, GPD1, TGM1, CPAMD8, THRAP3, LAMA3, C14ORF159, FREM2, STAC2, GSTM3, JPH1, SHD, HGD, GPC5, DOK7, STAC3, BCL2L13, KCTD12, BPGM, TUBA1A, GALNT3, GPT, HNRNPL, DKK1, PLEKHG1, ARHGAP8, CEMIP, WDR83, NTN1, MEI, BAG2, CACNA1H, RABEPK, SLC9A3R1, TPCN2, PDIA3, LGALS9, RANGRF, LSS, PPP2R3B, SPG20, TM7SF2, EIF2AK2, PSMB8, SLC38A5, TLCD1, FRAT2, SKAP2, CDH2, ASL, FMN2, ARPP21, TPGS1, FAM60A, PLA2G6, PSMB10, COX7A2, SCARA5, DLL1, TLE3, LFNG, MTTP, TMEM198B, PLXNB3, SPON2, ANXA3, SLC35D1, C11ORF54, PTPRE, and a combination thereof.

[0056] In some embodiments, the altered cell line and / or the altered expression profile comprises a change to a gene, a transcript, or a protein selected from the group consisting of ABCG2, SI, NDUFS8, ITGA5, CNTD1, PKHD1L1, PLXNB2, CASP10, FN1, ASAP2, IL13RA2, DAAM2, MCTP1, NUGGC, MEGF10, KIAA1324L, CPXM1, PHACTR4, FGF13, FLT1, PRICKLEI, ZEB1, SULF2, NET1, KIFAP3, HDAC9, DOPEY2, MAN2B2, TLE4, GARNL3, PFKP, ANKS1B, ABHD4, GTPBP2, PLXNA3, CREB3, NLRP12, PTPRK, RGN, GLUL, MMP13, CMYA5, CAMTAI, ABCA1, CDH1, EPHA10, DCHS1, OLFML1, SLC12A5, F8, ARHGAP22, LTBP3, PPP1R42, ADH5, REEP1, ADAMTS1, ATF5, ALDH1L1, ADAMTSL3, CSF1R, BSCL2, SLC15A2, CYP3A4, KIAA1644, ABCC6, GARS, ANTXRL, GGT7, P2RY4, IL1B, PRKAG2, TNFAIP3, VASP, FSTL1, KLHL38, SLC47A2, SLC5A5, FKBP14, MAGI2, GTPBP1, EXOC3L1, RAB37, KRT12, SLCO2B1, ADM2, DACT2, CHRD, ROBO3, MMP19, PTK7, PLEKHH1, FERMT1, SRPX2, TOX3, CTSS, MST1R, CCDC108, SEMA6C, AVPR1A, TSC22D4, FSTL3, ITGA2, PTGIS, COLEC12, NLN, FBXO32, CCDC153, DOCKIO, CYSTM1, FAM214A, CAND2, ARHGEF25, PTPLAD2, PAMR1, ULK2, PRODH, KRT8, TRIM55, KIAA1522, OPLAH, PREXI, LRP2, TBC1D2, INVS, ADAMTS12, MDM2, CSRNP1, RTP4, MED13L, NFKBIA, RGS12, LMNA, RIN1, TCN2, PDE7B, COL23A1, KIAA0141, AATK, IL1RAP, MXRA8, ZMIZ1, TMTC2, ISG15, MAP6, ACSL3, MKL2, ATXN1, WDFY2, CAPN2, ERRFI1, FARP1, HFE2, ZC3H12D, UAP1L1, RNF165, MPP5, SAT1, HBP1, AMPD2, HOMEZ, B3GNT2, STEAP4, PCDHAC2, COL4A3BP, TNS3, RNF169, AEBP1, TFE3, TTYH1, NEIL1, KIAA1033, MMP14, ACSL4, KLHL40, LPIN1, FGD1, XPC,TNFAIP2, CCDC92, DAB2, MTMR11, ZFYVE28, PC, ADIPOR2, MYODI, ZBTB33, METRNL, TBC1D2B, MFAP5, SCD, PPP1R3C, VPS4B, QPCT,CTSH, ARHGAP24, WDFY4, ROR2, ATP6V1B2, CTSZ, CXADR, MFSD2A, AVIL, XKRX, CHRNG, TIFA, TMCC3, SEMA4B, GDF10, PARD3, MAN2B1, PNPLA6, COL15A1, VPS41, TBC1D26, GHDC, HEY1, SCUBE3, MYLPF, MARCKSL1, RAB11FIP1, NTN1, GPT, GPD1, BAIAP2, MFI2, IPO13, ARHGEF28, ATP2A1, SORBS2, AD API, TLE3, C11ORF54, CD58, MOG, DPYS15, HNRNPL, PDIA3, PLXNB3, HUNK, HEY1, IFI27L2, ARHGAP6, SPON2, LFNG, HSD3B7, TMEM200B, AB AT, KCTD12, GSTM3, TNNI3, SEMA3E, HES1, UCP2, GALNT15, ADPRHL1, ANO8, SKAP2, COX7A2, DKK1, RABEPK, SHD, CEMIP, XYLT1, CPAMD8, PSMB8, FBP1, DLL1, TLCD1, ANKRD24, GALNT3, BCL2L13, THRAP3, SCARA5, MTTP, RANGRF, WDR83, ASL, PSMB10, SLC12A8, TM7SF2, ANXA3, LAMA3, FREM2, FAM60A, MYO16, ZEB2, STAC3, HYAL2, EMD, CDH2, CRAT, MEI, PLA2G6, LGALS9, DOK7, HIST1H1E, FRAT2, SLC35D1, BAG2,C14ORF159, SLC45A3, FMN2, STAC2, TTC28, SLC38A5, PTPRE, LSS, AM0TL2, CACNA1H, GPC5, SLC9A3R1, TPGS1, ARPP21, PLEKHG1, TUBA1A, EIF2AK2, MURC, JPH1, PPP2R3B, BPGM, ARHGAP8, TPCN2, ARSI, IER2, SPG20, TMEM198B, HGD, ALAS1, TGM1, and a combination thereof.

[0057] In some embodiments, the method for generating an altered cell line comprises an altered cell line comprising a gene, a transcript, or a protein selected from the group consisting of ABCG2, SI, NDUFS8, ITGA5, CNTD1, PKHD1L1, PLXNB2, CASP10, FN1, ASAP2, IL13RA2, DAAM2, MCTP1, NUGGC, MEGF10, KIAA1324L, CPXM1, PHACTR4, FGF13, FLT1, PRICKLEI, ZEB1, SULF2, NET1, KIFAP3, HDAC9, DOPEY2, MAN2B2, TLE4, GARNL3, PFKP, ANKS1B, ABHD4, GTPBP2, PLXNA3, CREB3, NLRP12, PTPRK, RGN, and a combination thereof.

[0058] In some embodiments, the altered cell line and / or the altered expression profile comprises a change to comprises a change to a gene, a transcript, or a protein selected from the group consisting of ABCG2, SI, NDUFS8, ITGA5, CNTD1, PKHD1L1, PLXNB2, CASP10, FN1, ASAP2, IL13RA2, DAAM2, MCTP1, NUGGC, MEGF10, KIAA1324L, CPXM1, PHACTR4, FGF13, FLT1, PRICKLEI, ZEB1, SULF2, NET1, KIFAP3, HDAC9, DOPEY2, MAN2B2, TLE4, GARNL3, PFKP, ANKS1B, ABHD4, GTPBP2, PLXNA3, CREB3, NLRP12, PTPRK, RGN, GLUL, and a combination thereof. In certain embodiments, the change to the selected gene, transcript, or protein comprises a genetic variant comprising a deleterious effect on the resulting protein, compared to an effect of a non-variant gene of a corresponding or reference non-altered cell line or a reference genome. In certain embodiments, the change to the selected gene, transcript, or protein comprises a genetic variant comprising a frameshift, a nonsense, a stop codon, or a loss of function mutation. In certain embodiments, the deleterious effect comprises protein truncation, loss of protein function, and / or triggering of nonsense-mediated protein decay. In certain embodiments, the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is upregulated by a change of 0.5 to about 14 log fold, about 0.5 to about 12 log fold, 0.5 to about 10 log fold, about 0.5 to about 8 log fold, about 0.5 to about 6 log fold, about 0.5 to about 4 log fold, or about 0.5 to about 2 log fold, each inclusive, compared to a reference expression level of the selected gene. In certain embodiments, the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is upregulated by a change of about 1.0 log fold, about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, 5.0 log fold, about 5.5 log fold, about 6.0 log fold,about 6.5 log fold, 7.0 log fold, about 7.5 log fold, about 8.0 log fold, about 8.5 log fold, about 9.0 log fold, about 9.5 log fold, or about 10.0 log fold, compared to a reference expression level of the selected gene.

[0059] In some embodiments, the method for generating an altered cell line comprises an altered cell line comprising a gene, a transcript, or a protein selected from the group consisting of GLUL, ABCG2, SI, MMP13, CMYA5, CAMTAI, ABCA1, CDH1, NDUFS8, EPHA10, DCHS1, OLFML1, ITGA5, SLC12A5, F8, CNTD1, PKHD1L1, ARHGAP22, LTBP3, PPP1R42, ADH5, REEP1, ADAMTS1, ATF5, ALDH1L1, ADAMTSL3, PLXNB2, CASP10, CSF1R, BSCL2, SLC15A2, CYP3A4, FN1, KIAA1644, ABCC6, GARS, ANTXRL, ASAP2, GGT7, GARS, P2RY4, ABCA1, IL1B, PRKAG2, TNFAIP3, VASP, FSTL1, IL13RA2, KLHL38, SLC47A2, SLC5A5, FKBP14, MAGI2, GTPBP1, DAAM2, EXOC3L1, RAB37, KRT12, SLCO2B1, ADM2, MCTP1, DACT2, NUGGC, CHRD, ROBO3, MMP19, PTK7, PLEKHH1, MEGF10, FERMT1, SRPX2, TOX3, CTSS, MST1R, CCDC108, SEMA6C, AVPR1A, TSC22D4, FSTL3, ITGA2, PTGIS, COLEC12, KIAA1324L, NLN, FBXO32, CCDC153, CPXM1, PHACTR4, FGF13, DOCK10, CYSTM1, FAM214A, CAND2, ARHGEF25, PTPLAD2, PAMR1, ULK2, PRODH, KRT8, TRIM55, KIAA1522, OPLAH, PREXI, LRP2, TBC1D2, INVS, FLT1, PRICKLEI, ADAMTS12, MDM2, CSRNP1, RTP4, MED13L, NFKBIA, RGS12, LMNA, RIN1, TCN2, PDE7B, COL23A1, KIAA0141, ANTXRL, AATK, ZEB1, IL1RAP, COL23A1, SULF2, MXRA8, ZMIZ1, TMTC2, KIFAP3, ISG15, MAP6, HDAC9, ACSL3, DOPEY2, MAN2B2, GARNL3, MKL2, ATXN1, WDFY2, CAPN2, ERRFI1, FARP1, HFE2, ZC3H12D, PFKP, ANKS1B, UAP1L1, ABHD4, RNF165, MPP5, SAT1, HBP1, AMPD2, HOMEZ, B3GNT2, GTPBP2, STEAP4, PCDHAC2, COL4A3BP, TNS3, RNF169, AEBP1, TFE3, TTYH1, NEIL1, KIAA1033, MMP14, ACSL4, KLHL40, LPIN1, FGD1, XPC, PLXNA3, TNFAIP2, CCDC92, DAB2, MTMR11, ZFYVE28, PC, ADIPOR2, MYODI, ZBTB33, METRNL, TBC1D2B, MFAP5, SCD, PPP1R3C, VPS4B, QPCT, METRNL, CTSH, CREB3, ARHGAP24, WDFY4, ROR2, ATP6V1B2, CTSZ, CXADR, MFSD2A, AVIL, XKRX, NLRP12, PTPRK, CHRNG, TIFA, TMCC3, SEMA4B, GDF10, PARD3, RGN, MAN2B1, PNPLA6, COL15A1, VPS41, TBC1D26, GHDC, ATHL1, NUGGC, TBC1D26, FSTL3, PNPLA6, XKRX, LTBP3, MFAP5, ABCC6, CSF1R, FARP1, SRPX2, LRP2, AATK, KRT12, MCTP1, CCDC153, SLC5A5, KRT8, PAMR1, FN1, and a combination thereof.

[0060] In some embodiments, the altered cell line and / or the altered expression profile comprises a change to a gene, a transcript, or a protein selected from the group consisting of GLUL, ABCG2, SI, MMP13, CMYA5, CAMTAI, ABCA1, CDH1, NDUFS8, EPHA10,DCHS1, 0LFML1, ITGA5, SLC12A5, F8, CNTD1, PKHD1L1, ARHGAP22, LTBP3, PPP1R42, ADH5, REEP1, ADAMTS1, ATF5, ALDH1L1, ADAMTSL3, PLXNB2, CASP10, CSF1R, BSCL2, SLC15A2, CYP3A4, FN1, KIAA1644, ABCC6, GARS, ANTXRL, ASAP2, GGT7, GARS, P2RY4, ABCA1, IL1B, PRKAG2, TNFAIP3, VASP, FSTL1, IL13RA2, KLHL38, SLC47A2, SLC5A5, FKBP14, MAGI2, GTPBP1, DAAM2, EXOC3L1, RAB37, KRT12, SLCO2B1, ADM2, MCTP1, DACT2, NUGGC, CHRD, ROBO3, MMP19, PTK7, PLEKHH1, MEGF10, FERMT1, SRPX2, TOX3, CTSS, MST1R, CCDC108, SEMA6C, AVPR1A, TSC22D4, FSTL3, ITGA2, PTGIS, COLEC12, KIAA1324L, NLN, FBXO32, CCDC153, CPXM1, PHACTR4, FGF13, DOCKIO, CYSTM1, FAM214A, CAND2, ARHGEF25, PTPLAD2, PAMR1, ULK2, PRODH, KRT8, TRIM55, KIAA1522, OPLAH, PREXI, LRP2, TBC1D2, INVS, FLT1, PRICKLEI, ADAMTS12, MDM2, CSRNP1, RTP4, MED13L, NFKBIA, RGS12, LMNA, RIN1, TCN2, PDE7B, COL23A1, KIAA0141, ANTXRL, AATK, ZEB1, IL1RAP, COL23A1, SULF2, MXRA8, ZMIZ1, TMTC2, KIFAP3, ISG15, MAP6, HDAC9, ACSL3, DOPEY2, MAN2B2, GARNL3, MKL2, ATXN1, WDFY2, CAPN2, ERRFI1, FARP1, HFE2, ZC3H12D, PFKP, ANKS1B, UAP1L1, ABHD4, RNF165, MPP5, SAT1, HBP1, AMPD2, HOMEZ, B3GNT2, GTPBP2, STEAP4, PCDHAC2, COL4A3BP, TNS3, RNF169, AEBP1, TFE3, TTYH1, NEIL1, KIAA1033, MMP14, ACSL4, KLHL40, LPIN1, FGD1, XPC, PLXNA3, TNFAIP2, CCDC92, DAB2, MTMR11, ZFYVE28, PC, ADIPOR2, MYODI, ZBTB33, METRNL, TBC1D2B, MFAP5, SCD, PPP1R3C, VPS4B, QPCT, METRNL, CTSH, CREB3, ARHGAP24, WDFY4, ROR2, ATP6V1B2, CTSZ, CXADR, MFSD2A, AVIL, XKRX, NLRP12, PTPRK, CHRNG, TIFA, TMCC3, SEMA4B, GDF10, PARD3, RGN, MAN2B1, PNPLA6, COL15A1, VPS41, TBC1D26, GHDC, ATHL1, and a combination thereof. In certain embodiments, the change to the selected gene, transcript, or protein comprises a genetic variant comprising a non-deleterious effect on the resulting protein, compared an effect of a non-variant gene of a corresponding or reference non-altered cell line or a reference genome. In certain embodiments, the change to the selected gene, transcript, or protein comprises a genetic variant comprising an intragenic or an intron variant. In specific embodiments, the non-deleterious effect comprises an alteration or a change in effectiveness of the resulting protein. In particular embodiments, the effectiveness of the resulting protein is decreased. In particular embodiments, the effectiveness of the resulting protein is increased. In certain embodiments, the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is upregulated by a change of about 0.5 to about 14 log fold, about 0.5 to about 12 log fold, 0.5 to about 10 logfold, about 0.5 to about 8 log fold, about 0.5 to about 6 log fold, about 0.5 to about 4 log fold, or about 0.5 to about 2 log fold, each inclusive, compared to a reference expression level of the selected gene. In certain embodiments, the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is upregulated by a change of about 1.0 log fold, about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, 7.0 log fold, about 7.5 log fold, about 8.0 log fold, about 8.5 log fold, about 9.0 log fold, about 9.5 log fold, or about 10.0 log fold, compared to a reference expression level of the selected gene.

[0061] In some embodiments, the method for generating an altered cell line comprises an altered cell line comprising a gene, a transcript, or a protein selected from the group consisting of HEY1, SCUBE3, MYLPF, MARCKSL1, RAB11FIP1, NTN1, GPT, GPD1, BAIAP2, MFI2, IPO13, ARHGEF28, ATP2A1, SORBS2, AD API, TLE3, C11ORF54, CD58, MOG, DPYS15, HNRNPL, PDIA3, PLXNB3, HUNK, and a combination thereof.

[0062] In some embodiments, the altered cell line and / or the altered expression profile comprises a change to a gene, a transcript, or a protein selected from the group consisting of HEY1, SCUBE3, MYLPF, MARCKSL1, RAB11FIP1, NTN1, GPT, GPD1, BAIAP2, MFI2, IPO13, ARHGEF28, ATP2A1, SORBS2, AD API, TLE3, C11ORF54, CD58, MOG, DPYS15, HNRNPL, PDIA3, PLXNB3, HUNK, and a combination thereof. In certain embodiments, the change to the selected gene, transcript, or protein comprises a genetic variant comprising a deleterious effect on the resulting protein, compared to an effect of a non-variant gene of a corresponding or reference non-altered cell line or a reference genome. In certain embodiments, the change to the selected gene, transcript, or protein comprises a genetic variant comprising a frameshift, a nonsense, a stop codon, or a loss of function mutation. In certain embodiments, the deleterious effect comprises protein truncation, loss of protein function, and / or triggering of nonsense-mediated protein decay. In certain embodiments, the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is downregulated by a change of 0.5 to about 14 log fold, about 0.5 to about 12 log fold, 0.5 to about 10 log fold, about 0.5 to about 8 log fold, about 0.5 to about 6 log fold, about 0.5 to about 4 log fold, or about 0.5 to about 2 log fold, each inclusive, compared to a reference expression level of the selected gene. In certain embodiments, the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is downregulated by a change of about 1.0 log fold, about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, 3.0 log fold,about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, 7.0 log fold, about 7.5 log fold, about 8.0 log fold, about 8.5 log fold, about 9.0 log fold, about 9.5 log fold, or about 10.0 log fold, compared to a reference expression level of the selected gene.

[0063] In some embodiments, the method for generating an altered cell line comprises an altered cell line comprising a gene, a transcript, or a protein selected from the group consisting of HEY1, IFI27L2, ARHGAP6, SPON2, SCUBE3, MYLPF, LFNG, HSD3B7, TMEM200B, ABAT, KCTD12, GSTM3, TNNI3, SEMA3E, HES1, UCP2, GALNT15, ADPRHL1, MARCKSL1, RAB11FIP1, AN08, NTN1, SKAP2, GPT, COX7A2, DKK1, GPD1, BAIAP2, RABEPK, SHD, CEMIP, XYLT1, CPAMD8, PSMB8, FBP1, DLL1, MFI2, TLCD1, IPO13, ANKRD24, GALNT3, ARHGEF28, BCL2L13, THRAP3, SCARA5, MTTP, RANGRF, ATP2A1, WDR83, SORBS2, ASL, PSMB10, SLC12A8, TM7SF2, AD API, ANXA3, LAMA3, TLE3, FREM2, FAM60A, C11ORF54, MY016, CD58, ZEB2, STAC3, HYAL2, EMD, CDH2, CRAT, MEI, PLA2G6, LGALS9, D0K7, MOG, HIST1H1E, FRAT2, SLC35D1, BAG2, HNRNPL, C14ORF159, SLC45A3, FMN2, STAC2, TTC28, SLC38A5, PTPRE, LSS, AMOTL2, CACNA1H, GPC5, SLC9A3R1, TPGS1, ARPP21, PLEKHG1, TUBA1A, EIF2AK2, MURC, JPH1, PPP2R3B, BPGM, ARHGAP8, TPCN2, PDIA3, ARSI, IER2, PLXNB3, SPG20, TMEM198B, HUNK, HGD, ALAS1 TGM1, and a combination thereof.

[0064] In certain embodiments, the altered expression profile comprises a change to a gene, a transcript, or a protein selected from the group consisting of HEY1, IFI27L2, ARHGAP6, SPON2, SCUBE3, MYLPF, LFNG, HSD3B7, TMEM200B, ABAT, KCTD12, GSTM3, TNNI3, SEMA3E, HES1, UCP2, GALNT15, ADPRHL1, MARCKSL1, RAB11FIP1, ANO8, NTN1, SKAP2, GPT, COX7A2, DKK1, GPD1, BAIAP2, RABEPK, SHD, CEMIP, XYLT1, CPAMD8, PSMB8, FBP1, DLL1, MFI2, TLCD1, IPO13, ANKRD24, GALNT3, ARHGEF28, BCL2L13, THRAP3, SCARA5, MTTP, RANGRF, ATP2A1, WDR83, SORBS2, ASL, PSMB10, SLC12A8, TM7SF2, AD API, ANXA3, LAMA3, TLE3, FREM2, FAM60A, C11ORF54, MY016, CD58, ZEB2, STAC3, HYAL2, EMD, CDH2, CRAT, MEI, PLA2G6, LGALS9, DOK7, MOG, HIST1H1E, FRAT2, SLC35D1, BAG2, HNRNPL, C14ORF159, SLC45A3, FMN2, STAC2, TTC28, SLC38A5, PTPRE, LSS, AMOTL2, CACNA1H, GPC5, SLC9A3R1, TPGS1, ARPP21, PLEKHG1, TUBA1A, EIF2AK2, MURC, JPH1, PPP2R3B, BPGM, ARHGAP8, TPCN2, PDIA3, ARSI, IER2, PLXNB3, SPG20, TMEM198B, HUNK, HGD, ALAS1, TGM1, and a combination thereof. In certain embodiments, the change to the selected gene, transcript, or proteincomprises a genetic variant comprising a non-deleterious effect on the resulting protein, compared an effect of a non-variant gene of a corresponding or reference non-altered cell line or a reference genome. In certain embodiments, the change to the selected gene, transcript, or protein comprises a genetic variant comprising an intragenic or an intron variant. In specific embodiments, the non-deleterious effect comprises an alteration or a change in effectiveness of the resulting protein. In particular embodiments, the effectiveness of the resulting protein is decreased. In particular embodiments, the effectiveness of the resulting protein is increased. In certain embodiments, the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is downregulated by a change of about 0.5 to about 14 log fold, about 0.5 to about 12 log fold, 0.5 to about 10 log fold, about 0.5 to about 8 log fold, about 0.5 to about 6 log fold, about 0.5 to about 4 log fold, or about 0.5 to about 2 log fold, each inclusive, compared to a reference expression level of the selected gene. In certain embodiments, the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is downregulated by a change of about 1.0 log fold, about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, 7.0 log fold, about 7.5 log fold, about 8.0 log fold, about 8.5 log fold, about 9.0 log fold, about 9.5 log fold, or about 10.0 log fold, compared to a reference expression level of the selected gene.

[0065] In some embodiments, the method for generating an altered cell line comprises contacting the adherent cell line with a vector construct carrying a heterologous gene, wherein expression of the heterologous gene modifies the expression profile of the altered cell line. In some embodiments, the process sufficient to generate the altered cell line comprises contacting the adherent cell line with a vector construct carrying a heterologous gene, wherein expression of the heterologous gene effects a modified expression profile of the altered cell line.

[0066] In some embodiments the expression profile comprises an upregulated gene expression profile. In some embodiments, the expression profile comprises a downregulated gene expression profile. In some embodiments the vector construct comprises a DNA vector. In some embodiments, the vector construct comprises an RNA vector. In some embodiments, the vector construct is a non- viral vector selected from the group consisting of a cosmid, a yeast artificial chromosome, a bacterial artificial chromosome, a shuttle vector, a plasmid vector, a secretion vector, and any combination thereof. In some embodiments, the vectorconstruct is a viral vector selected from the group consisting of a retrovirus vector, an adeno- associated virus vector, an adenovirus vector, a herpesvirus vector, and a poxvirus vector.

[0067] In some embodiments, the method for generating an altered cell line comprises forced, transient, non-integrative gene expression using various nucleic acid molecules comprising contacting the adherent cell line with messenger ribonucleic acid (mRNA), complementary deoxyribonucleic acid (cDNA), micro RNA (miRNA), transfer RNA (tRNA), silencing RNA (siRNA), or any variants, combinations, or analogs thereof, wherein delivery of the nucleic acid molecules into the cell are not integrated into the genome of the cell, and wherein delivery of the nucleic acid molecules effects a modified expression profile in the altered cell.

[0068] In some embodiments, the method for generating an altered cell line comprises altering, silencing, attenuating, or knocking out a gene or genetic construct in order to modulate the expression profile of the altered cell line. In some embodiments, the process sufficient to generate an altered cell line comprises altering, silencing, attenuating, and / or knocking out a gene or genetic construct to effect a modified expression profile of the altered cell line. In some embodiments, mutagenesis techniques comprising site-directed mutagenesis using error-prone PCR or oligonucleotide-directed mutagenesis are employed.BRIEF DESCRIPTION OF THE DRAWINGS

[0069] The present application can be understood by reference to the following description taken in conjunction with the accompanying figures.

[0070] FIGS. 1A-1E show the phenotype of attached bluefin tuna (BFT) primary myoblast cells in 2D culture. FIG. 1A and FIG. IB are brightfield microscope images showing the 2D phenotype of BFT adherent cells at 10X (FIG. 1A) and 20X (FIG. IB) magnification. FIGS. 1C-1E are graphs showing cell number and death upon transition to suspension without prior treatment for twelve different cell lines. All twelve cell lines failed to transition into a viable suspension cell line. Each graph (FIGS. 1C-1E) represents an experiment and every line in a graph denotes a different cell line in the experiment.

[0071] FIGS. 2A-2C show the behavior of two different suspension cell lines generated from the same parent adherent cell line under different conditions, of which only one cell line successfully transitioned to suspension. FIG. 2A shows a graph displaying the percentages, out of the total number of cells, of suspension versus adherent cells after trypsinization for the “suspension” cell line that failed to grow in suspension. FIG. 2B shows a graph displaying the percentages, out of the total number of cells, of suspension versus adherent cells aftertrypsinization for the “suspension” cell line that successfully developed into a suspension cell line. FIG. 2C is a brightfield microscope image showing the phenotype of the cell line that successfully transitioned into a suspension cell line (featured in FIG. 2B) at 4X magnification.

[0072] FIGS. 3A-3C show characteristics of two suspension cell lines that successfully transitioned from adherent to suspension cell lines (“Cell line 1 Suspension cells” transitioned from parent “Cell line 1 Adherent cells” and “Cell line 2 Suspension cells” transitioned from parent “Cell line 2 Adherent cells”). FIG. 3A shows a graph displaying the percentage, out of the total number of cells, of suspension versus adherent cells after trypsinization of the two cell lines that successfully transitioned into suspension cell lines. FIGS. 3B and 3C are brightfield microscope images showing the phenotypes of the two successful suspension cell lines at 4X magnification (scale bar = 130 pm).

[0073] FIGS. 4A and 4B are Venn diagrams showing the analysis of genome changes and gene expression changes that are specific to the suspension cell lines. FIG. 4A shows the intersection(s) among genes that exhibit high genome variance, genes with significant gene expression upregulation, and genes with significant downregulation. 40 upregulated genes found in one of the intersections have been tabulated and can be found in Table 1 in Example 3. 24 downregulated genes found in the other intersection have been tabulated and can be found in Table 3 in Example 3. FIG. 4B shows the intersection(s) among genes that exhibit moderate genome variance, genes with significant gene expression upregulation and, genes with significant downregulation. 219 upregulated genes found in one of the two intersections have been tabulated and can be found in Table 2 in Example 3. 112 downregulated genes found in the other intersection have been tabulated and can be found in Table 4 in Example 3.DETAILED DESCRIPTION

[0074] Certain exemplary embodiments are described to provide an overall understanding of the principles of the altered cell lines, growth medium, and methods of generating the altered cells. Those skilled in the art will understand that the disclosures described herein and illustrated in the accompanying drawings are non-limiting exemplary embodiments. The features illustrated or described in connection with one exemplary embodiment may be combined with the features of other embodiments. The embodiments are not limited to specific compositions, cell types, cell lines, cell culture methods of preparing suchcompositions, or uses thereof. Such modifications and variations are intended to be included within the scope of the present disclosure.

[0075] The terminology used herein is for the purpose of describing aspects only and is not intended to be limiting. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs.

[0076] The disclosure herein is predicated, in part, on the surprising discovery that BFT cells can be adapted to suspension growth in serum-free medium, and that altered BFT cells are capable of exhibiting an altered expression profile as compared to an expression profile of a corresponding non-altered cell line.

[0077] The present disclosure provides metabolically intact and stable aquatic suspension cell lines adapted from adherent cell lines that can be grown in suspension culture without supporting material. Such suspension cell lines can be useful for long-term propagation and to produce cell-based seafood.

[0078] The novel suspension cell line(s) and method(s) disclosed herein provide for suspension cell lines that have demonstrated extraordinary performance relative to an adherent or parent cell line from which it was derived. The suspension cell lines described herein also exhibit altered gene expression compared to the adherent cell from which they were derived.

[0079] The present disclosure also allows the adaptation of adherent cell lines, primary cell lines, and / or stem cells to suspension cell culture in a serum-free medium. Moreover, the disclosure enables cell lines to continuously grow in suspension without a change in differential state.

[0080] Compared with commonly used techniques, the disclosed method improves high throughput application, sustainability, and efficiency. Known methods of preparing suspension cells from adherent mammalian cell lines rely predominately on the use of microbeads, microcarriers, and other similar devices. By employing the disclosed method, it is possible to eliminate the costly compound serum from the cell culture media, which has made high throughput applications for cell lines cost-prohibitive heretofore. In particular, the disclosure provides a method for fast establishment of serum-free suspension cell lines that do not require microbeads, microcarriers, and other similar devices.

[0081] In addition, microbeads and microcarriers are extremely expensive, therefore the method(s) of the disclosure— which does not rely upon microbeads and / or microcarriers— has reduced cost over traditional methods which require microcarriers and / or microbeads.

[0082] The ability of cells to grow in suspension is preferred due to ease of scale-up optimization. The disclosed method can be used to generate suspension cell lines for seafood-based industry applications.

[0083] Provided herein are compositions wherein the composition may comprise an altered cell line that has an altered expression profile as compared to an expression profile of a corresponding non-altered cell line, wherein the altered cell line is a suspension cell line. .Also provided herein are compositions wherein the composition may comprise an altered cell line that has an altered expression profile as compared to an expression profile of a reference non-altered cell line, wherein the altered cell line is a suspension cell line.

[0084] Provided herein are methods for (a) providing an adherent cell line or derivative thereof; and (b) subjecting the adherent cell line or derivative thereof to a process sufficient to generate an altered cell line comprising an altered expression profile comprising: (1) an altered gene expression profile that is different than a gene expression profile of the adherent cell line or derivative used in (a) and / or a reference non-altered cell line; and / or (2) an altered phenotypic profile that is different than a phenotypic profile of the adherent cell line or derivative used in (a) and / or a reference non-altered cell line.

[0085] In some embodiments, the altered expression profile comprises an altered gene expression profile and / or an altered phenotypic profile. In some embodiments, the altered phenotypic profile comprise of improved viability and stable growth rates in (1) nonadherent, suspension cell culture, (2) serum-free media cell culture, and / or (3) animal component-free media cell culture. In specific embodiments, the altered phenotypic profile comprises of improved viability and stabilized growth rates in non-adherent, suspension cell culture. In specific embodiments, the altered phenotypic profile comprises of improved viability and stabilized growth rates in serum-free media cell culture. In specific embodiments, the altered phenotypic profile comprises of improved viability and stabilized growth rates in animal component-free media culture.

[0086] In some embodiments, the improvement in viability of the altered cell line is demonstrated by the percentage of the total number of suspension cell in culture. In some embodiments, for the altered cell line, between about 30% to about 100% of the total cells in culture, about 40% to about 100% of the total cells in culture, about 50% to about 100% of the total cells in culture, about 60% to about 100 % of the total cells in culture, about 70% to about 100% of the total cells in culture, about 80% to about 100% of the total cells in culture, about 90% to about 100% of the total cells in culture, each inclusive, are suspension cells. In some embodiments, for the altered cell line, between about 0% to about 50% of the total cellsin culture, about 10% to about 50% of the total cells in culture, about 20% to about 50% of the total cells in culture, about 30% to about 50% of the total cells in culture, about 40% to about 50% of the total cells in culture, 0% to about 40% of the total cells in culture, about 10% to about 40% of the total cells in culture, about 20% to about 40% of the total cells in culture, about 30% to about 40% of the total cells in culture, about 0% to about 30% of the total cells in culture, about 10% to about 30% of the total cells in culture, about 20% to about 30% of total cells in culture, or about 10% to about 20% of the total cells in culture, each inclusive, are adherent cells.

[0087] In some embodiments, the stabilized growth rate of the altered cell line is demonstrated by the percentage of the total number of suspension cell in culture after a certain number of days in suspension. In some embodiments, for the altered cell line, between about 30% to about 100% of the total cells, about 40% to about 100% of the total cells, about 50% to about 100% of the total cells, about 60% to about 100 % of the total cells, about 70% to about 100% of the total cells, about 80% to about 100% of the total cells, about 90% to about 100% of the total cells, each inclusive, are suspension cells after about 20 to about 180 days in suspension, about 40 to about 180 days in suspension, about 60 to about 180 days in suspension, about 80 to about 180 days in suspension, about 100 to about 180 days in suspension, about 120 to about 180 days in suspension, about 140 to about 180 days in suspension, about 160 to about 180 days in suspension, 20 to about 160 days in suspension, about 40 to about 160 days in suspension, about 60 to about 160 days in suspension, about 80 to about 160 days in suspension, about 100 to about 160 days in suspension, about 120 to about 160 days in suspension, about 140 to about 160 days in suspension, 20 to about 140 days in suspension, about 40 to about 140 days in suspension, about 60 to about 140 days in suspension, about 80 to about 140 days in suspension, about 100 to about 140 days in suspension, about 120 to about 140 days in suspension, 20 to about 120 days in suspension, about 40 to about 120 days in suspension, about 60 to about 120 days in suspension, about 80 to about 120 days in suspension, about 100 to about 120 days in suspension, 20 to about 100 days in suspension, about 40 to about 100 days in suspension, about 60 to about 100 days in suspension, about 80 to about 100 days in suspension, 20 to about 80 days in suspension, about 40 to about 80 days in suspension, about 60 to about 80 days in suspension, 20 to about 60 days in suspension, about 40 to about 60 days in suspension, about 20 to about 40 days in suspension, each inclusive. In specific embodiments, more than 50% of the total cells are suspension cells after about 60 days or more, 70 days or more, 80 days or more, 90 days or more, or 100 days or more of culture. Insome embodiments, for the altered cell line, between about 0% to about 50% of the total cells in culture, about 10% to about 50% of the total cells, about 20% to about 50% of the total cells, about 30% to about 50% of the total cells, about 40% to about 50% of the total cells, 0% to about 40% of the total cells, about 10% to about 40% of the total cells, about 20% to about 40% of the total cells, about 30% to about 40% of the total cells, about 0% to about 30% of the total cells, about 10% to about 30% of the total cells, about 20% to about 30% of total cells, or about 10% to about 20% of the total cells, each inclusive, are adherent cells after about 20 to about 180 days in suspension, about 40 to about 180 days in suspension, about 60 to about 180 days in suspension, about 80 to about 180 days in suspension, about 100 to about 180 days in suspension, about 120 to about 180 days in suspension, about 140 to about 180 days in suspension, about 160 to about 180 days in suspension, 20 to about 160 days in suspension, about 40 to about 160 days in suspension, about 60 to about 160 days in suspension, about 80 to about 160 days in suspension, about 100 to about 160 days in suspension, about 120 to about 160 days in suspension, about 140 to about 160 days in suspension, 20 to about 140 days in suspension, about 40 to about 140 days in suspension, about 60 to about 140 days in suspension, about 80 to about 140 days in suspension, about 100 to about 140 days in suspension, about 120 to about 140 days in suspension, 20 to about 120 days in suspension, about 40 to about 120 days in suspension, about 60 to about 120 days in suspension, about 80 to about 120 days in suspension, about 100 to about 120 days in suspension, 20 to about 100 days in suspension, about 40 to about 100 days in suspension, about 60 to about 100 days in suspension, about 80 to about 100 days in suspension, 20 to about 80 days in suspension, about 40 to about 80 days in suspension, about 60 to about 80 days in suspension, 20 to about 60 days in suspension, about 40 to about 60 days in suspension, about 20 to about 40 days in suspension, each inclusive. In specific embodiments, less than 50% of the total cells are adherent cells after about 60 days or more, 70 days or more, 80 days or more, 90 days or more, or 100 days or more of culture.

[0088] In some embodiments, the altered expression profile comprises an upregulated gene expression profile. In some embodiments, the altered expression profile comprises a downregulated gene expression profile.

[0089] In some embodiments, the altered cell line comprises a change to a gene, a transcript, or a protein selected from the group consisting of ABCG2, SI, NDUFS8, ITGA5, CNTD1, PKHD1L1, PLXNB2, CASP10, FN1, ASAP2, IL13RA2, DAAM2, MCTP1, NUGGC, MEGF10, KIAA1324L, CPXM1, PHACTR4, FGF13, FLT1, PRICKLEI, ZEB1, SULF2, NET1, KIFAP3, HDAC9, DOPEY2, MAN2B2, TLE4, GARNL3, PFKP, ANKS1B,ABHD4, GTPBP2, PLXNA3, CREB3, NLRP12, PTPRK, RGN, GLUL, MMP13, CMYA5, CAMTAI, ABCA1, CDH1, EPHA10, DCHS1, OLFML1, SLC12A5, F8, ARHGAP22, LTBP3, PPP1R42, ADH5, REEP1, ADAMTS1, ATF5, ALDH1L1, ADAMTSL3, CSF1R, BSCL2, SLC15A2, CYP3A4, KIAA1644, ABCC6, GARS, ANTXRL, GGT7, P2RY4, IL1B, PRKAG2, TNFAIP3, VASP, FSTL1, KLHL38, SLC47A2, SLC5A5, FKBP14, MAGI2, GTPBP1, EXOC3L1, RAB37, KRT12, SLCO2B1, ADM2, DACT2, CHRD, ROBO3, MMP19, PTK7, PLEKHH1, FERMT1, SRPX2, TOX3, CTSS, MST1R, CCDC108, SEMA6C, AVPR1A, TSC22D4, FSTL3, ITGA2, PTGIS, COLEC12, NLN, FBXO32, CCDC153, DOCKIO, CYSTM1, FAM214A, CAND2, ARHGEF25, PTPLAD2, PAMR1, ULK2, PRODH, KRT8, TRIM55, KIAA1522, OPLAH, PREXI, LRP2, TBC1D2, INVS, ADAMTS12, MDM2, CSRNP1, RTP4, MED13L, NFKBIA, RGS12, LMNA, RIN1, TCN2, PDE7B, COL23A1, KIAA0141, AATK, IL1RAP, MXRA8, ZMIZ1, TMTC2, ISG15, MAP6, ACSL3, MKL2, ATXN1, WDFY2, CAPN2, ERRFI1, FARP1, HFE2, ZC3H12D, UAP1L1, RNF165, MPP5, SAT1, HBP1, AMPD2, HOMEZ, B3GNT2, STEAP4, PCDHAC2, COL4A3BP, TNS3, RNF169, AEBP1, TFE3, TTYH1, NEIL1, KIAA1033, MMP14, ACSL4, KLHL40, LPIN1, FGD1, XPC,TNFAIP2, CCDC92, DAB2, MTMR11, ZFYVE28, PC, ADIPOR2, MYODI, ZBTB33, METRNL, TBC1D2B, MFAP5, SCD, PPP1R3C, VPS4B, QPCT,CTSH, ARHGAP24, WDFY4, ROR2, ATP6V1B2, CTSZ, CXADR, MFSD2A, AVIL, XKRX, CHRNG, TIFA, TMCC3, SEMA4B, GDF10, PARD3, MAN2B1, PNPLA6, COL15A1, VPS41, TBC1D26, GHDC, HEY1, SCUBE3, MYLPF, MARCKSL1, RAB11FIP1, NTN1, GPT, GPD1, BAIAP2, MFI2, IPO13, ARHGEF28, ATP2A1, SORBS2, AD API, TLE3, C11ORF54, CD58, MOG, DPYS15, HNRNPL, PDIA3, PLXNB3, HUNK, HEY1, IFI27L2, ARHGAP6, SPON2, LFNG, HSD3B7, TMEM200B, ABAT, KCTD12, GSTM3, TNNI3, SEMA3E, HES1, UCP2, GALNT15, ADPRHL1, ANO8, SKAP2, COX7A2, DKK1, RABEPK, SHD, CEMIP, XYLT1, CPAMD8, PSMB8, FBP1, DLL1, TLCD1, ANKRD24, GALNT3, BCL2L13, THRAP3, SCARA5, MTTP, RANGRF, WDR83, ASL, PSMB10, SLC12A8, TM7SF2, ANXA3, LAMA3, FREM2, FAM60A, MYO16, ZEB2, STAC3, HYAL2, EMD, CDH2, CRAT, MEI, PLA2G6, LGALS9, DOK7, HIST1H1E, FRAT2, SLC35D1, BAG2, C14ORF159, SLC45A3, FMN2, STAC2, TTC28, SLC38A5, PTPRE, LSS, AMOTL2, CACNA1H, GPC5, SLC9A3R1, TPGS1, ARPP21, PLEKHG1, TUBA1A, EIF2AK2, MURC, JPH1, PPP2R3B, BPGM, ARHGAP8, TPCN2, ARSI, IER2, SPG20, TMEM198B, HGD, ALAS1, TGM1, and a combination thereof.

[0090] In some embodiments, the altered expression profile comprises a change to a gene, a transcript, or a protein selected from the group consisting of ABCG2, SI, NDUFS8, ITGA5, CNTD1, PKHD1L1, PLXNB2, CASP10, FN1, ASAP2, IL13RA2, DAAM2, MCTP1, NUGGC, MEGF10, KIAA1324L, CPXM1, PHACTR4, FGF13, FLT1, PRICKLEI, ZEB1, SULF2, NET1, KIFAP3, HDAC9, DOPEY2, MAN2B2, TLE4, GARNL3, PFKP, ANKS1B, ABHD4, GTPBP2, PLXNA3, CREB3, NLRP12, PTPRK, RGN, GLUL, MMP13, CMYA5, CAMTAI, ABCA1, CDH1, EPHA10, DCHS1, OLFML1, SLC12A5, F8, ARHGAP22, LTBP3, PPP1R42, ADH5, REEP1, ADAMTS1, ATF5, ALDH1L1, ADAMTSL3, CSF1R, BSCL2, SLC15A2, CYP3A4, KIAA1644, ABCC6, GARS, ANTXRL, GGT7, P2RY4, IL1B, PRKAG2, TNFAIP3, VASP, FSTL1, KLHL38, SLC47A2, SLC5A5, FKBP14, MAGI2, GTPBP1, EXOC3L1, RAB37, KRT12, SLCO2B1, ADM2, DACT2, CHRD, ROBO3, MMP19, PTK7, PLEKHH1, FERMT1, SRPX2, TOX3, CTSS, MST1R, CCDC108, SEMA6C, AVPR1A, TSC22D4, FSTL3, ITGA2, PTGIS, COLEC12, NLN, FBXO32, CCDC153, DOCKIO, CYSTM1, FAM214A, CAND2, ARHGEF25, PTPLAD2, PAMR1, ULK2, PRODH, KRT8, TRIM55, KIAA1522, OPLAH, PREXI, LRP2, TBC1D2, INVS, ADAMTS12, MDM2, CSRNP1, RTP4, MED13L, NFKBIA, RGS12, LMNA, RIN1, TCN2, PDE7B, COL23A1, KIAA0141, AATK, IL1RAP, MXRA8, ZMIZ1, TMTC2, ISG15, MAP6, ACSL3, MKL2, ATXN1, WDFY2, CAPN2, ERRFI1, FARP1, HFE2, ZC3H12D, UAP1L1, RNF165, MPP5, SAT1, HBP1, AMPD2, HOMEZ, B3GNT2, STEAP4, PCDHAC2, COL4A3BP, TNS3, RNF169, AEBP1, TFE3, TTYH1, NEIL1, KIAA1033, MMP14, ACSL4, KLHL40, LPIN1, FGD1, XPC,TNFAIP2, CCDC92, DAB2, MTMR11, ZFYVE28, PC, ADIPOR2, MYODI, ZBTB33, METRNL, TBC1D2B, MFAP5, SCD, PPP1R3C, VPS4B, QPCT,CTSH, ARHGAP24, WDFY4, ROR2, ATP6V1B2, CTSZ, CXADR, MFSD2A, AVIL, XKRX, CHRNG, TIFA, TMCC3, SEMA4B, GDF10, PARD3, MAN2B1, PNPLA6, COL15A1, VPS41, TBC1D26, GHDC, HEY1, SCUBE3, MYLPF, MARCKSL1, RAB11FIP1, NTN1, GPT, GPD1, BAIAP2, MFI2, IPO13, ARHGEF28, ATP2A1, SORBS2, AD API, TLE3, C11ORF54, CD58, MOG, DPYS15, HNRNPL, PDIA3, PLXNB3, HUNK, HEY1, IFI27L2, ARHGAP6, SPON2, LFNG, HSD3B7, TMEM200B, ABAT, KCTD12, GSTM3, TNNI3, SEMA3E, HES1, UCP2, GALNT15, ADPRHL1, ANO8, SKAP2, COX7A2, DKK1, RABEPK, SHD, CEMIP, XYLT1, CPAMD8, PSMB8, FBP1, DLL1, TLCD1, ANKRD24, GALNT3, BCL2L13, THRAP3, SCARA5, MTTP, RANGRF, WDR83, ASL, PSMB10, SLC12A8, TM7SF2, ANXA3, LAMA3, FREM2, FAM60A, MYO16, ZEB2, STAC3, HYAL2, EMD, CDH2, CRAT, MEI, PLA2G6, LGALS9, DOK7, HIST1H1E, FRAT2, SLC35D1, BAG2, C14ORF159, SLC45A3, FMN2,STAC2, TTC28, SLC38A5, PTPRE, LSS, AM0TL2, CACNA1H, GPC5, SLC9A3R1, TPGS1, ARPP21, PLEKHG1, TUBA1A, EIF2AK2, MURC, JPH1, PPP2R3B, BPGM, ARHGAP8, TPCN2, ARSI, IER2, SPG20, TMEM198B, HGD, ALAS1, TGM1, and a combination thereof.

[0091] In some embodiments, the altered cell line comprises a change to a gene, a transcript, or a protein selected from the group consisting of ABCG2, SI, NDUFS8, ITGA5, CNTD1, PKHD1L1, PLXNB2, CASP10, FN1, ASAP2, IL13RA2, DAAM2, MCTP1, NUGGC, MEGF10, KIAA1324L, CPXM1, PHACTR4, FGF13, FLT1, PRICKLEI, ZEB1, SULF2, NET1, KIFAP3, HDAC9, DOPEY2, MAN2B2, TLE4, GARNL3, PFKP, ANKS1B, ABHD4, GTPBP2, PLXNA3, CREB3, NLRP12, PTPRK, RGN, GLUL, and a combination thereof. In some embodiments, the altered gene expression profile comprises a change to a gene, a transcript, or a protein selected from the group consisting of ABCG2, SI, NDUFS8, ITGA5, CNTD1, PKHD1L1, PLXNB2, CASP10, FN1, ASAP2, IL13RA2, DAAM2, MCTP1, NUGGC, MEGF10, KIAA1324L, CPXM1, PHACTR4, FGF13, FLT1, PRICKLEI, ZEB1, SULF2, NET1, KIFAP3, HDAC9, DOPEY2, MAN2B2, TLE4, GARNL3, PFKP, ANKS1B, ABHD4, GTPBP2, PLXNA3, CREB3, NLRP12, PTPRK, RGN, GLUL, and a combination thereof.

[0092] In certain embodiments, the change to the selected gene, transcript, or protein comprises a genetic variant comprising a deleterious effect on the resulting protein, compared to an effect of a non-variant gene of a corresponding or reference non-altered cell line or a reference genome. In certain embodiments, the change to the selected gene, transcript, or protein comprises a genetic variant comprising a frameshift, a nonsense, a stop codon, or a loss of function mutation. In specific embodiments, the change to the selected gene, transcript, or protein comprises a genetic variant comprising a frameshift mutation. In specific embodiments, the change to the selected gene, transcript, or protein comprises a genetic variant comprising a nonsense mutation. In specific embodiments, the change to the selected gene, transcript, or protein comprises a genetic variant comprising a stop codon mutation. In specific embodiments, the change to the selected gene, transcript, or protein comprises a genetic variant comprising a loss of function mutation. In certain embodiments, the deleterious effect comprises protein truncation, loss of protein function, and / or triggering of nonsense-mediated protein decay. In specific embodiments, the deleterious effect comprises protein truncation. In specific embodiments, the deleterious effect comprises loss of protein function. In specific embodiments, the deleterious effect comprises triggering of nonsense-mediated protein decay.

[0093] In certain embodiments, the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is upregulated by a change of 0.5 to about 14 log fold, about 0.5 to about 12 log fold, 0.5 to about 10 log fold, about 0.5 to about 8 log fold, about 0.5 to about 6 log fold, about 0.5 to about 4 log fold, or about 0.5 to about 2 log fold, each inclusive, compared to a reference expression level of the selected gene. In certain embodiments, the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is upregulated by a change of about 1.0 log fold, about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, 7.0 log fold, about 7.5 log fold, about 8.0 log fold, about 8.5 log fold, about 9.0 log fold, about 9.5 log fold, or about 10.0 log fold, compared to a reference expression level of the selected gene.

[0094] In specific embodiments, the selected gene is ABCG2 and ABCG2 is upregulated by a change in expression level of about 3 log fold to about 11 log fold, about 3 log fold to about 9 log fold, about 3 log fold to about 7 log fold, about 3 log fold to about 5 log fold, about 5 log fold to about 11 log fold, about 5 log fold to about 9 log fold, about 5 log fold to about 7 log fold, about 7 log fold to about 11 log fold, about 7 log fold to about 9 log fold, or about 9 log fold to about 11 log fold, each inclusive, compared to a reference expression level of ABCG2. In particular embodiments, the change in expression level is about 5 log fold to about 9 log fold. In specific embodiments, the selected gene is ABCG2 and ABCG2 is upregulated by about a change in expression level of about 4.0 log fold, about 4.5 log fold, about 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, about 7 log fold, about 7.5 log fold, about 8 log fold, about 8.5 log fold, about 9 log fold, about 9.5 log fold, or about 10 log fold, compared to a reference expression level of ABCG2. In particular embodiments, the change in expression level is about 8.8 log fold. In particular embodiments, the change in expression level is about 5.1 log fold.

[0095] In specific embodiments, the selected gene is SI and SI is upregulated by a change in expression level of about 1 log fold to about 11 log fold, about 1 log fold to about 9 log fold, about 1 log fold to about 7 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, about 3 log fold to about 11 log fold, about 3 log fold to about 9 log fold, about 3 log fold to about 7 log fold, about 3 log fold to about 5 log fold, about 5 log fold to about 11 log fold, about 5 log fold to about 9 log fold, about 5 log fold to about 7 log fold, about 7 log fold to about 11 log fold, about 7 log fold to about 9 log fold, or about 9 log fold to about 11 log fold, each inclusive, compared to a reference expression level of SI. Inparticular embodiments, the change in expression level is about 2 log fold to about 9 log fold. In specific embodiments, the selected gene is SI and SI is upregulated by about a change in expression level of about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, about 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, about 7 log fold, about 7.5 log fold, about 8 log fold, about 8.5 log fold, about 9 log fold, about 9.5 log fold, or about 10 log fold, compared to a reference expression level of SI. In particular embodiments, the change in expression level is about 8.6 log fold. In particular embodiments, the change in expression level is about 2.7 log fold.

[0096] In specific embodiments, the selected gene is NDUFS8 and NDUFS8 is upregulated by a change in expression level of about 1 log fold to about 9 log fold, about 1 log fold to about 7 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, about 3 log fold to about 9 log fold, about 3 log fold to about 7 log fold, about 3 log fold to about 5 log fold, about 5 log fold to about 9 log fold, about 5 log fold to about 7 log fold, or about 7 log fold to about 9 log fold, each inclusive, compared to a reference expression level of NDUFS8. In particular embodiments, the change in expression level is about 1 log fold to about 7.5 log fold. In specific embodiments, the selected gene is NDUFS8 and NDUFS8 is upregulated by about a change in expression level of about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, about 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, about 7 log fold, about 7.5 log fold, about 8 log fold, or about 8.5 log fold, compared to a reference expression level of NDUFS8. In particular embodiments, the change in expression level is about 6.7 log fold. In particular embodiments, the change in expression level is about 1.3 log fold.

[0097] In specific embodiments, the selected gene is ITGA5 and ITGA5 is upregulated by a change in expression level of about 1 log fold to about 9 log fold, about 1 log fold to about 7 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, about 3 log fold to about 9 log fold, about 3 log fold to about 7 log fold, about 3 log fold to about 5 log fold, about 5 log fold to about 9 log fold, about 5 log fold to about 7 log fold, or about 7 log fold to about 9 log fold, each inclusive, compared to a reference expression level of ITGA5. In particular embodiments, the change in expression level is about 1 log fold to about 7 log fold. In specific embodiments, the selected gene is ITGA5 and ITGA5 is upregulated by about a change in expression level of about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 2.0 log fold, about 2.5 logfold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, about 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, about 7 log fold, about 7.5 log fold, about 8 log fold, or about 8.5 log fold, compared to a reference expression level of ITGA5. In particular embodiments, the change in expression level is about 6.0 log fold. In particular embodiments, the change in expression level is about 1.9 log fold.

[0098] In specific embodiments, the selected gene is CNTD1 and CNTD1 is upregulated by a change in expression level of about 1 log fold to about 7 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, about 3 log fold to about 7 log fold, about 3 log fold to about 5 log fold, or about 5 log fold to about 7 log fold, each inclusive, compared to a reference expression level of CNTD1. In particular embodiments, the change in expression level is about 1 log fold to about 6.5 log fold. In specific embodiments, the selected gene is CNTD1 and CNTD1 is upregulated by about a change in expression level of about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, about 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, about 7 log fold, about 7.5 log fold, or about 8 log fold, compared to a reference expression level of CNTD1. In particular embodiments, the change in expression level is about 5.6 log fold. In particular embodiments, the change in expression level is about 2.6 log fold.

[0099] In specific embodiments, the selected gene is PKHD1L1 and PKHD1L1 is upregulated by a change in expression level of about 1 log fold to about 7 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, about 3 log fold to about 7 log fold, about 3 log fold to about 5 log fold, or about 5 log fold to about 7 log fold, each inclusive, compared to a reference expression level of PKHD1L1. In particular embodiments, the change in expression level is about 1 log fold to about 6.5 log fold. In specific embodiments, the selected gene is PKHD1L1 and PKHD1L1 is upregulated by about a change in expression level of about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, about 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, about 7 log fold, about 7.5 log fold, or about 8 log fold, compared to a reference expression level of PKHD1L1. In particular embodiments, the change in expression level is about 5.5 log fold. In particular embodiments, the change in expression level is about 5.4 log fold.

[0100] In specific embodiments, the selected gene is PLXNB2 and PLXNB2 is upregulated by a change in expression level of about 1 log fold to about 7 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, about 3 log fold to about 7log fold, about 3 log fold to about 5 log fold, or about 5 log fold to about 7 log fold, each inclusive, compared to a reference expression level of PLXNB2. In particular embodiments, the change in expression level is about 1 log fold to about 5.5 log fold. In specific embodiments, the selected gene is PLXNB2 and PLXNB2 is upregulated by about a change in expression level of about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, about 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, or about 7 log fold, compared to a reference expression level of PLXNB2. In particular embodiments, the change in expression level is about 4.5 log fold. In particular embodiments, the change in expression level is about 1.5 log fold.

[0101] In specific embodiments, the selected gene is CASP10 and CASP10 is upregulated by a change in expression level of about 1 log fold to about 7 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, about 3 log fold to about 7 log fold, about 3 log fold to about 5 log fold, or about 5 log fold to about 7 log fold, each inclusive, compared to a reference expression level of CASP10. In particular embodiments, the change in expression level is about 1 log fold to about 5 log fold. In specific embodiments, the selected gene is CASP10 and CASP10 is upregulated by about a change in expression level of about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, about 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, or about 7 log fold, compared to a reference expression level of CASP10. In particular embodiments, the change in expression level is about 4.3 log fold. In particular embodiments, the change in expression level is about 2.1 log fold.

[0102] In specific embodiments, the selected gene is FN1 and FN1 is upregulated by a change in expression level of about 1 log fold to about 9 log fold, about 1 log fold to about 7 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, about 3 log fold to about 9 log fold, about 3 log fold to about 7 log fold, about 3 log fold to about 5 log fold, about 5 log fold to about 11 log fold, about 5 log fold to about 9 log fold, about 5 log fold to about 7 log fold, or about 7 log fold to about 9 log fold, each inclusive, compared to a reference expression level of FN1. In particular embodiments, the change in expression level is about 1 log fold to about 7 log fold. In specific embodiments, the selected gene is FN1 and FN1 is upregulated by about a change in expression level of about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, about 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, about 7log fold, about 7.5 log fold, about 8.0 log fold, about 8.5 log fold, or about 9 log fold, compared to a reference expression level of FN1. In particular embodiments, the change in expression level is about 4.1 log fold. In particular embodiments, the change in expression level is about 5.0 log fold.

[0103] In specific embodiments, the selected gene is ASAP2 and ASAP2 is upregulated by a change in expression level of about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of ASAP2. In particular embodiments, the change in expression level is about 1 log fold to about 5 log fold. In specific embodiments, the selected gene is ASAP2 and ASAP2 is upregulated by about a change in expression level of about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of ASAP2. In particular embodiments, the change in expression level is about 3.5 log fold. In particular embodiments, the change in expression level is about 1.7 log fold.

[0104] In specific embodiments, the selected gene is IL13RA2 and IL13RA2 is upregulated by a change in expression level of about 1 log fold to about 7 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, about 3 log fold to about 7 log fold, about 3 log fold to about 5 log fold, or about 5 log fold to about 7 log fold, each inclusive, compared to a reference expression level of IL13RA2. In particular embodiments, the change in expression level is about 1 log fold to about 7 log fold. In specific embodiments, the selected gene is IL13RA2 and IL13RA2 is upregulated by about a change in expression level of about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, about 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, or about 7 log fold, compared to a reference expression level of IL13RA2. In particular embodiments, the change in expression level is about 3.6 log fold. In particular embodiments, the change in expression level is about 5.7 log fold.

[0105] In specific embodiments, the selected gene is DAAM2 and DAAM2 is upregulated by a change in expression level of about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of DAAM2. In particular embodiments, the change in expression level is about 1 log fold to about 4.5 log fold. In specific embodiments, theselected gene is DAAM2 and DAAM2 is upregulated by about a change in expression level of about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about4.5 log fold, or about 5.0 log fold, compared to a reference expression level of DAAM2. In particular embodiments, the change in expression level is about 3.3 log fold. In particular embodiments, the change in expression level is about 1.8 log fold.

[0106] In specific embodiments, the selected gene is MCTP1 and MCTP1 is upregulated by a change in expression level of about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of MCTP1. In particular embodiments, the change in expression level is about 1 log fold to about 5 log fold. In specific embodiments, the selected gene is MCTP1 and MCTP1 is upregulated by about a change in expression level of about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of MCTP1. In particular embodiments, the change in expression level is about 3.1 log fold. In particular embodiments, the change in expression level is about 3.0 log fold.

[0107] In specific embodiments, the selected gene is NUGGC and NUGGC is upregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of NUGGC. In particular embodiments, the change in expression level is about 0.5 log fold to about 4.0 log fold. In specific embodiments, the selected gene is NUGGC and NUGGC is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 log fold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of NUGGC. In particular embodiments, the change in expression level is about 3.1 log fold. In particular embodiments, the change in expression level is about 1 log fold.

[0108] In specific embodiments, the selected gene is MEGF10 and MEGF10 is upregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of MEGF10. In particular embodiments, the change in expression level is about 0.5 log fold to about 4.0 log fold. In specific embodiments, the selected gene is MEGF10 and MEGF10 is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 log fold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of MEGF10. In particular embodiments, the change in expression level is about 3.0 log fold. In particular embodiments, the change in expression level is about 1 log fold.

[0109] In specific embodiments, the selected gene is KIAA1324L and KIAA1324L is upregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of KIAA1324L. In particular embodiments, the change in expression level is about 0.5 log fold to about 4.0 log fold. In specific embodiments, the selected gene is KIAA1324L and KIAA1324L is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 log fold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of KIAA1324L. In particular embodiments, the change in expression level is about 2.8 log fold. In particular embodiments, the change in expression level is about 2.9 log fold.

[0110] In specific embodiments, the selected gene is CPXM1 and CPXM1 is upregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive,compared to a reference expression level of CPXM1. In particular embodiments, the change in expression level is about 0.5 log fold to about 3.5 log fold. In specific embodiments, the selected gene is CPXM1 and CPXM1 is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 log fold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of CPXM1. In particular embodiments, the change in expression level is about 2.7 log fold. In particular embodiments, the change in expression level is about 2.0 log fold.

[0111] In specific embodiments, the selected gene is PHACTR4 and PHACTR4 is upregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of PHACTR4. In particular embodiments, the change in expression level is about 0.5 log fold to about 3.5 log fold. In specific embodiments, the selected gene is PHACTR4 and PHACTR4 is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 log fold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of PHACTR4. In particular embodiments, the change in expression level is about 2.6 log fold. In particular embodiments, the change in expression level is about 1.6 log fold.

[0112] In specific embodiments, the selected gene is FGF13 and FGF13 is upregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of FGF13. In particular embodiments, the change in expression level is about 1.5 log fold to about 5 log fold. In specific embodiments, the selected gene is FGF13 and FGF13 is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 logfold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of FGF13. In particular embodiments, the change in expression level is about 2.6 log fold. In particular embodiments, the change in expression level is about 3.7 log fold.

[0113] In specific embodiments, the selected gene is FLT1 and FLT1 is upregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of FLT1. In particular embodiments, the change in expression level is about 1.0 log fold to about 4.5 log fold. In specific embodiments, the selected gene is FLT1 and FLT1 is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 log fold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of FLT1. In particular embodiments, the change in expression level is about 2.3 log fold. In particular embodiments, the change in expression level is about 3.1 log fold.

[0114] In specific embodiments, the selected gene is PRICKLEI and PRICKLEI is upregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of PRICKLEI. In particular embodiments, the change in expression level is about 0.5 log fold to about 3.5 log fold. In specific embodiments, the selected gene is PRICKLEI and PRICKLEI is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 log fold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of PRICKLEI. In particular embodiments, thechange in expression level is about 2.3 log fold. In particular embodiments, the change in expression level is about 1.1 log fold.

[0115] In specific embodiments, the selected gene is ZEB1 and ZEB1 is upregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of ZEB1. In particular embodiments, the change in expression level is about 0.5 log fold to about 3.5 log fold. In specific embodiments, the selected gene is ZEB1 and ZEB1 is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 log fold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of ZEB1. In particular embodiments, the change in expression level is about 2.2 log fold. In particular embodiments, the change in expression level is about 1.5 log fold.

[0116] In specific embodiments, the selected gene is SULF2 and SULF2 is upregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of SULF2. In particular embodiments, the change in expression level is about 0.5 log fold to about 3.5 log fold. In specific embodiments, the selected gene is SULF2 and SULF2 is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 log fold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of SULF2. In particular embodiments, the change in expression level is about 2.2 log fold. In particular embodiments, the change in expression level is about 1.4 log fold.

[0117] In specific embodiments, the selected gene is NET1 and NET1 is upregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold,about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of NET1. In particular embodiments, the change in expression level is about 0.5 log fold to about 3.5 log fold. In specific embodiments, the selected gene is NET1 and NET1 is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 log fold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of NET1. In particular embodiments, the change in expression level is about 2.1 log fold. In particular embodiments, the change in expression level is about 1.9 log fold.

[0118] In specific embodiments, the selected gene is KIFAP3 and KIFAP3 is upregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of KIFAP3. In particular embodiments, the change in expression level is about 0.5 log fold to about 3.5 log fold. In specific embodiments, the selected gene is KIFAP3 and KIFAP3 is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 log fold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of KIFAP3. In particular embodiments, the change in expression level is about 2.1 log fold. In particular embodiments, the change in expression level is about 1.2 log fold.

[0119] In specific embodiments, the selected gene is HDAC9 and HDAC9 is upregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of HDAC9. In particular embodiments, the change in expression level is about 0.5 log fold to about 3.5 log fold. In specific embodiments, the selected gene is HDAC9 and HDAC9 is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 logfold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of HDAC9. In particular embodiments, the change in expression level is about 2.0 log fold. In particular embodiments, the change in expression level is about 1.5 log fold.

[0120] In specific embodiments, the selected gene is DOPEY2 and DOPEY2 is upregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of DOPEY2. In particular embodiments, the change in expression level is about 0.5 log fold to about 3.5 log fold. In specific embodiments, the selected gene is DOPEY2 and DOPEY2 is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 log fold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of DOPEY2. In particular embodiments, the change in expression level is about 2.0 log fold. In particular embodiments, the change in expression level is about 1.1 log fold.

[0121] In specific embodiments, the selected gene is MAN2B2 and MAN2B2 is upregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of MAN2B2. In particular embodiments, the change in expression level is about 0.5 log fold to about 3.5 log fold. In specific embodiments, the selected gene is MAN2B2 and MAN2B2 is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 log fold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold,compared to a reference expression level of MAN2B2. In particular embodiments, the change in expression level is about 2.0 log fold. In particular embodiments, the change in expression level is about 2.1 log fold.

[0122] In specific embodiments, the selected gene is TLE4 and TLE4 is upregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of TLE4. In particular embodiments, the change in expression level is about 0.5 log fold to about 4.5 log fold. In specific embodiments, the selected gene is TLE4 and TLE4 is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 log fold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of TLE4. In particular embodiments, the change in expression level is about 2.0 log fold. In particular embodiments, the change in expression level is about 3.3 log fold.

[0123] In specific embodiments, the selected gene is GARNL3 and GARNL3 is upregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of GARNL3. In particular embodiments, the change in expression level is about 0.5 log fold to about 3.5 log fold. In specific embodiments, the selected gene is GARNL3 and GARNL3 is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 log fold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of GARNL3. In particular embodiments, the change in expression level is about 2.0 log fold. In particular embodiments, the change in expression level is about 2.4 log fold.

[0124] In specific embodiments, the selected gene is PFKP and PFKP is upregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold toabout 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of PFKP. In particular embodiments, the change in expression level is about 0.5 log fold to about 3 log fold. In specific embodiments, the selected gene is PFKP and PFKP is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 log fold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of PFKP. In particular embodiments, the change in expression level is about 1.9 log fold. In particular embodiments, the change in expression level is about 2.0 log fold.

[0125] In specific embodiments, the selected gene is ANKS1B and ANKS1B is upregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of ANKS1B. In particular embodiments, the change in expression level is about 0.5 log fold to about 3 log fold. In specific embodiments, the selected gene is ANKS1B and ANKS1B is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 log fold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of PFKP. In particular embodiments, the change in expression level is about 1.9 log fold. In particular embodiments, the change in expression level is about 1.1 log fold.

[0126] In specific embodiments, the selected gene is ANKS1B and ANKS1B is upregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of ANKS1B. In particular embodiments, the change in expression level is about 0.5 log fold to about 3 log fold. In specific embodiments, the selected gene is ANKS1B and ANKS1B is upregulated by about achange in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 log fold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of ANKS1B. In particular embodiments, the change in expression level is about 1.9 log fold. In particular embodiments, the change in expression level is about 1.1 log fold.

[0127] In specific embodiments, the selected gene is ABHD4 and ABHD4 is upregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of ABHD4. In particular embodiments, the change in expression level is about 0.5 log fold to about 3 log fold. In specific embodiments, the selected gene is ABHD4 and ABHD4 is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 log fold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of ABHD4. In particular embodiments, the change in expression level is about 1.8 log fold. In particular embodiments, the change in expression level is about 1.2 log fold.

[0128] In specific embodiments, the selected gene is GTPBP2 and GTPBP2 is upregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of GTPBP2. In particular embodiments, the change in expression level is about 0.5 log fold to about 3 log fold. In specific embodiments, the selected gene is GTPBP2 and GTPBP2 is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 log fold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of GTPBP2. In particular embodiments, the change in expression level is about 1.6 log fold. In particular embodiments, the change in expression level is about 1.3 log fold.

[0129] In specific embodiments, the selected gene is PLXNA3 and PLXNA3 is upregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of PLXNA3. In particular embodiments, the change in expression level is about 0.5 log fold to about 3 log fold. In specific embodiments, the selected gene is PLXNA3 and PLXNA3 is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 log fold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of PLXNA3. In particular embodiments, the change in expression level is about 1.5 log fold. In particular embodiments, the change in expression level is about 2 log fold.

[0130] In specific embodiments, the selected gene is CREB3 and CREB3 is upregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of CREB3. In particular embodiments, the change in expression level is about 0.5 log fold to about 3 log fold. In specific embodiments, the selected gene is CREB3 and CREB3 is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 log fold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of CREB3. In particular embodiments, the change in expression level is about 1.2 log fold. In particular embodiments, the change in expression level is about 1.5 log fold.

[0131] In specific embodiments, the selected gene is NLRP12 and NLRP12 is upregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of NLRP12. In particular embodiments, the change in expression level is about 0.5 log fold to about 2 log fold. In specific embodiments, the selected gene is NLRP12 and NLRP12 is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 log fold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, or about 4.5 log fold, compared to a reference expression level of NLRP12. In particular embodiments, the change in expression level is about 1.2 log fold. In particular embodiments, the change in expression level is about 1.1 log fold.

[0132] In specific embodiments, the selected gene is PTPRK and PTPRK is upregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of PTPRK. In particular embodiments, the change in expression level is about 0.5 log fold to about 2 log fold. In specific embodiments, the selected gene is PTPRK and PTPRK is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 log fold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, or about 4.5 log fold, compared to a reference expression level of PTPRK. In particular embodiments, the change in expression level is about 1.2 log fold. In particular embodiments, the change in expression level is about 1.2 log fold.

[0133] In specific embodiments, the selected gene is RGN and RGN is upregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of RGN. In particular embodiments, the change inexpression level is about 0.5 log fold to about 3 log fold. In specific embodiments, the selected gene is RGN and RGN is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 log fold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of RGN. In particular embodiments, the change in expression level is about 1.1 log fold. In particular embodiments, the change in expression level is about 1.9 log fold.

[0134] In some embodiments, the altered cell line comprises a change to a gene, a transcript, or a protein selected from the group consisting of GLUL, ABCG2, SI, MMP13, CMYA5, CAMTAI, ABCA1, CDH1, NDUFS8, EPHA10, DCHS1, OLFML1, ITGA5, SLC12A5, F8, CNTD1, PKHD1L1, ARHGAP22, LTBP3, PPP1R42, ADH5, REEP1, ADAMTS1, ATF5, ALDH1L1, ADAMTSL3, PLXNB2, CASP10, CSF1R, BSCL2, SLC15A2, CYP3A4, FN1, KIAA1644, ABCC6, GARS, ANTXRL, ASAP2, GGT7, GARS, P2RY4, ABCA1, IL1B, PRKAG2, TNFAIP3, VASP, FSTL1, IL13RA2, KLHL38, SLC47A2, SLC5A5, FKBP14, MAGI2, GTPBP1, DAAM2, EXOC3L1, RAB37, KRT12, SLCO2B1, ADM2, MCTP1, DACT2, NUGGC, CHRD, ROBO3, MMP19, PTK7, PLEKHH1, MEGF10, FERMT1, SRPX2, TOX3, CTSS, MST1R, CCDC108, SEMA6C, AVPR1A, TSC22D4, FSTL3, ITGA2, PTGIS, COLEC12, KIAA1324L, NLN, FBXO32, CCDC153, CPXM1, PHACTR4, FGF13, DOCK10, CYSTM1, FAM214A, CAND2, ARHGEF25, PTPLAD2, PAMR1, ULK2, PRODH, KRT8, TRIM55, KIAA1522, OPLAH, PREXI, LRP2, TBC1D2, INVS, FLT1, PRICKLEI, ADAMTS12, MDM2, CSRNP1, RTP4, MED13L, NFKBIA, RGS12, LMNA, RIN1, TCN2, PDE7B, COL23A1, KIAA0141, ANTXRL, AATK, ZEB1, IL1RAP, COL23A1, SULF2, MXRA8, ZMIZ1, TMTC2, KIFAP3, ISG15, MAP6, HDAC9, ACSL3, DOPEY2, MAN2B2, GARNL3, MKL2, ATXN1, WDFY2, CAPN2, ERRFI1, FARP1, HFE2, ZC3H12D, PFKP, ANKS1B, UAP1L1, ABHD4, RNF165, MPP5, SAT1, HBP1, AMPD2, HOMEZ, B3GNT2, GTPBP2, STEAP4, PCDHAC2, COL4A3BP, TNS3, RNF169, AEBP1, TFE3, TTYH1, NEIL1, KIAA1033, MMP14, ACSL4, KLHL40, LPIN1, FGD1, XPC, PLXNA3, TNFAIP2, CCDC92, DAB2, MTMR11, ZFYVE28, PC, ADIPOR2, MYODI, ZBTB33, METRNL, TBC1D2B, MFAP5, SCD, PPP1R3C, VPS4B, QPCT, METRNL, CTSH, CREB3, ARHGAP24, WDFY4, ROR2, ATP6V1B2, CTSZ, CXADR, MFSD2A, AVIL, XKRX, NLRP12, PTPRK, CHRNG, TIFA,TMCC3, SEMA4B, GDF10, PARD3, RGN, MAN2B1, PNPLA6, COL15A1, VPS41, TBC1D26, GHDC, ATHL1, and a combination thereof.

[0135] In some embodiments, the altered expression profile comprises a change to a gene, a transcript, or a protein selected from the group consisting of GLUL, ABCG2, SI, MMP13, CMYA5, CAMTAI, ABCA1, CDH1, NDUFS8, EPHA10, DCHS1, OLFML1, ITGA5, SLC12A5, F8, CNTD1, PKHD1L1, ARHGAP22, LTBP3, PPP1R42, ADH5, REEP1, ADAMTS1, ATF5, ALDH1L1, ADAMTSL3, PLXNB2, CASP10, CSF1R, BSCL2, SLC15A2, CYP3A4, FN1, KIAA1644, ABCC6, GARS, ANTXRL, ASAP2, GGT7, GARS, P2RY4, ABCA1, IL1B, PRKAG2, TNFAIP3, VASP, FSTL1, IL13RA2, KLHL38, SLC47A2, SLC5A5, FKBP14, MAGI2, GTPBP1, DAAM2, EXOC3L1, RAB37, KRT12, SLCO2B1, ADM2, MCTP1, DACT2, NUGGC, CHRD, ROBO3, MMP19, PTK7, PLEKHH1, MEGF10, FERMT1, SRPX2, TOX3, CTSS, MST1R, CCDC108, SEMA6C, AVPR1A, TSC22D4, FSTL3, ITGA2, PTGIS, COLEC12, KIAA1324L, NLN, FBXO32, CCDC153, CPXM1, PHACTR4, FGF13, DOCKIO, CYSTM1, FAM214A, CAND2, ARHGEF25, PTPLAD2, PAMR1, ULK2, PRODH, KRT8, TRIM55, KIAA1522, OPLAH, PREXI, LRP2, TBC1D2, INVS, FLT1, PRICKLEI, ADAMTS12, MDM2, CSRNP1, RTP4, MED13L, NFKBIA, RGS12, LMNA, RIN1, TCN2, PDE7B, COL23A1, KIAA0141, ANTXRL, AATK, ZEB1, IL1RAP, COL23A1, SULF2, MXRA8, ZMIZ1, TMTC2, KIFAP3, ISG15, MAP6, HDAC9, ACSL3, DOPEY2, MAN2B2, GARNL3, MKL2, ATXN1, WDFY2, CAPN2, ERRFI1, FARP1, HFE2, ZC3H12D, PFKP, ANKS1B, UAP1L1, ABHD4, RNF165, MPP5, SAT1, HBP1, AMPD2, HOMEZ, B3GNT2, GTPBP2, STEAP4, PCDHAC2, COL4A3BP, TNS3, RNF169, AEBP1, TFE3, TTYH1, NEIL1, KIAA1033, MMP14, ACSL4, KLHL40, LPIN1, FGD1, XPC, PLXNA3, TNFAIP2, CCDC92, DAB2, MTMR11, ZFYVE28, PC, ADIPOR2, MYODI, ZBTB33, METRNL, TBC1D2B, MFAP5, SCD, PPP1R3C, VPS4B, QPCT, METRNL, CTSH, CREB3, ARHGAP24, WDFY4, ROR2, ATP6V1B2, CTSZ, CXADR, MFSD2A, AVIL, XKRX, NLRP12, PTPRK, CHRNG, TIFA, TMCC3, SEMA4B, GDF10, PARD3, RGN, MAN2B1, PNPLA6, COL15A1, VPS41, TBC1D26, GHDC, ATHL1, and a combination thereof.

[0136] In certain embodiments, the change to the selected gene, transcript, or protein comprises a genetic variant comprising a non-deleterious effect on the resulting protein, compared an effect of a non-variant gene of a corresponding or reference non-altered cell line or a reference genome. In certain embodiments, the change to the selected gene, transcript, or protein comprises a genetic variant comprising an intragenic or an intron variant. In specific embodiments, the genetic variant comprises an intragenic variant. In specificembodiments, the genetic variant comprises an intron variant. In specific embodiments, the non-deleterious effect comprises an alteration or a change in effectiveness of the resulting protein. In particular embodiments, the effectiveness of the resulting protein is decreased. In particular embodiments, the effectiveness of the resulting protein is increased.

[0137] In certain embodiments, the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is upregulated by a change of about 0.5 to about 14 log fold, about 0.5 to about 12 log fold, 0.5 to about 10 log fold, about 0.5 to about 8 log fold, about 0.5 to about 6 log fold, about 0.5 to about 4 log fold, or about 0.5 to about 2 log fold, each inclusive, compared to a reference expression level of the selected gene. In certain embodiments, the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is upregulated by a change of about 1.0 log fold, about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, 7.0 log fold, about 7.5 log fold, about 8.0 log fold, about 8.5 log fold, about 9.0 log fold, about 9.5 log fold, or about 10.0 log fold, compared to a reference expression level of the selected gene.

[0138] In some embodiments, the altered cell line comprises a change to a gene, a transcript, or a protein selected from the group consisting of HEY1, SCUBE3, MYLPF, MARCKSL1, RAB11FIP1, NTN1, GPT, GPD1, BAIAP2, MFI2, IPO13, ARHGEF28, ATP2A1, SORBS2, AD API, TLE3, C11ORF54, CD58, MOG, DPYS15, HNRNPL, PDIA3, PLXNB3, HUNK, and a combination thereof.

[0139] In some embodiments, the altered expression profile comprises a change to a gene, a transcript, or a protein selected from the group consisting of HEY1, SCUBE3, MYLPF, MARCKSL1, RAB11FIP1, NTN1, GPT, GPD1, BAIAP2, MFI2, IPO13, ARHGEF28, ATP2A1, SORBS2, AD API, TLE3, C11ORF54, CD58, MOG, DPYS15, HNRNPL, PDIA3, PLXNB3, HUNK, and a combination thereof.

[0140] In certain embodiments, the change to the selected gene, transcript, or protein comprises a genetic variant comprising a deleterious effect on the resulting protein, compared to an effect of a non-variant gene of a corresponding or reference non-altered cell line or a reference genome. In certain embodiments, the change to the selected gene, transcript, or protein comprises a genetic variant comprising a frameshift, a nonsense, a stop codon, or a loss of function mutation. In certain embodiments, the deleterious effect comprises protein truncation, loss of protein function, and / or triggering of nonsense-mediated protein decay.

[0141] In certain embodiments, the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is downregulated by a change of 0.5 to about 14 log fold, about 0.5 to about 12 log fold, 0.5 to about 10 log fold, about 0.5 to about 8 log fold, about 0.5 to about 6 log fold, about 0.5 to about 4 log fold, or about 0.5 to about 2 log fold, each inclusive, compared to a reference expression level of the selected gene. In certain embodiments, the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is downregulated by a change of about 1.0 log fold, about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, 7.0 log fold, about 7.5 log fold, about 8.0 log fold, about 8.5 log fold, about 9.0 log fold, about 9.5 log fold, or about 10.0 log fold, compared to a reference expression level of the selected gene.

[0142] In specific embodiments, the selected gene is HEY 1 and HEY 1 is downregulated by a change in expression level of about 3 log fold to about 11 log fold, about 3 log fold to about 9 log fold, about 3 log fold to about 7 log fold, about 3 log fold to about 5 log fold, about 5 log fold to about 11 log fold, about 5 log fold to about 9 log fold, about 5 log fold to about 7 log fold, about 7 log fold to about 11 log fold, about 7 log fold to about 9 log fold, or about 9 log fold to about 11 log fold, each inclusive, compared to a reference expression level of HEY 1. In particular embodiments, the change in expression level is about 4 log fold to about 9 log fold. In specific embodiments, the selected gene is HEY1 and HEY1 is downregulated by about a change in expression level of about 4.0 log fold, about 4.5 log fold, about 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, about 7 log fold, about 7.5 log fold, about 8 log fold, about 8.5 log fold, about 9 log fold, about 9.5 log fold, or about 10 log fold, compared to a reference expression level of HEY 1. In particular embodiments, the change in expression level is about 5.3 log fold. In particular embodiments, the change in expression level is about 7 log fold.

[0143] In specific embodiments, the selected gene is SCUBE3 and SCUBE3 is downregulated by a change in expression level of about 1 log fold to about 9 log fold, about 1 log fold to about 7 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, about 3 log fold to about 9 log fold, about 3 log fold to about 7 log fold, about 3 log fold to about 5 log fold, about 5 log fold to about 9 log fold, about 5 log fold to about 7 log fold, or about 7 log fold to about 9 log fold, each inclusive, compared to a reference expression level of SCUBE3. In particular embodiments, the change in expression level is about 3 log fold to about 7 log fold. In specific embodiments, the selected gene is SCUBE3and SCUBE3 is downregulated by about a change in expression level of about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, about 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, about 7 log fold, about 7.5 log fold, about 8 log fold, or about 8.5 log fold, compared to a reference expression level of SCUBE3. In particular embodiments, the change in expression level is about 4.3 log fold. In particular embodiments, the change in expression level is about 5.1 log fold.

[0144] In specific embodiments, the selected gene is MYLPF and MYLPF is downregulated by a change in expression level of about 1 log fold to about 7 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, about 3 log fold to about 7 log fold, about 3 log fold to about 5 log fold, or about 5 log fold to about 7 log fold, each inclusive, compared to a reference expression level of MYLPF. In particular embodiments, the change in expression level is about 3 log fold to about 7 log fold. In specific embodiments, the selected gene is MYLPF and MYLPF is downregulated by about a change in expression level of about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, about 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, about 7 log fold, about 7.5 log fold, or about 8 log fold, compared to a reference expression level of MYLPF. In particular embodiments, the change in expression level is about 4.1 log fold. In particular embodiments, the change in expression level is about 5.7 log fold.

[0145] In specific embodiments, the selected gene is MARCKSL1 and MARCKSL1 is downregulated by a change in expression level of about 1 log fold to about 7 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, about 3 log fold to about 7 log fold, about 3 log fold to about 5 log fold, or about 5 log fold to about 7 log fold, each inclusive, compared to a reference expression level of MARCKSL1. In particular embodiments, the change in expression level is about 1 log fold to about 5 log fold. In specific embodiments, the selected gene is MARCKSL1 and MARCKSL1 is downregulated by about a change in expression level of about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, about 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, or about 7 log fold, compared to a reference expression level of MARCKSL1. In particular embodiments, the change in expression level is about 3.0 log fold. In particular embodiments, the change in expression level is about 2.8 log fold.

[0146] In specific embodiments, the selected gene is RAB11FIP1 and RAB11FIP1 is downregulated by a change in expression level of about 1 log fold to about 7 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, about 3 log fold to about 7 log fold, about 3 log fold to about 5 log fold, or about 5 log fold to about 7 log fold, each inclusive, compared to a reference expression level of RAB 11FIP1. In particular embodiments, the change in expression level is about 1 log fold to about 5 log fold. In specific embodiments , the selected gene is RAB 11 FIP 1 and RAB 11 FIP 1 is downregulated by about a change in expression level of about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, about 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, or about 7 log fold, compared to a reference expression level of RAB 11FIP1. In particular embodiments, the change in expression level is about 2.9 log fold. In particular embodiments, the change in expression level is about 3.0 log fold.

[0147] In specific embodiments, the selected gene is NTN1 and NTN1 is downregulated by a change in expression level of about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of NTN1. In particular embodiments, the change in expression level is about 1 log fold to about 5 log fold. In specific embodiments, the selected gene is NTN1 and NTN1 is downregulated by about a change in expression level of about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of NTN1. In particular embodiments, the change in expression level is about 2.8 log fold. In particular embodiments, the change in expression level is about 1.4 log fold.

[0148] In specific embodiments, the selected gene is GPT and GPT is downregulated by a change in expression level of about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of GPT. In particular embodiments, the change in expression level is about 1 log fold to about 5 log fold. In specific embodiments, the selected gene is GPT and GPT is downregulated by about a change in expression level of about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold,compared to a reference expression level of GPT. In particular embodiments, the change in expression level is about 2.7 log fold. In particular embodiments, the change in expression level is about 1.5 log fold.

[0149] In specific embodiments, the selected gene is GPD1 and GPD1 is downregulated by a change in expression level of about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of GPD1. In particular embodiments, the change in expression level is about 1 log fold to about 5 log fold. In specific embodiments, the selected gene is GPD1 and GPD1 is downregulated by about a change in expression level of about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of GPD1. In particular embodiments, the change in expression level is about 2.6 log fold. In particular embodiments, the change in expression level is about 2.0 log fold.

[0150] In specific embodiments, the selected gene is BAIAP2 and BAIAP2 is downregulated by a change in expression level of about 1 log fold to about 7 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, about 3 log fold to about 7 log fold, about 3 log fold to about 5 log fold, or about 5 log fold to about 7 log fold, each inclusive, compared to a reference expression level of BAIAP2. In particular embodiments, the change in expression level is about 1 log fold to about 7 log fold. In specific embodiments, the selected gene is BAIAP2 and BAIAP2 is downregulated by about a change in expression level of about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, about 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, or about 7 log fold, compared to a reference expression level of BAIAP2. In particular embodiments, the change in expression level is about 2.6 log fold. In particular embodiments, the change in expression level is about 4.4 log fold.

[0151] In specific embodiments, the selected gene is MFI2 and MFI2 is downregulated by a change in expression level of about 1 log fold to about 7 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, about 3 log fold to about 7 log fold, about 3 log fold to about 5 log fold, or about 5 log fold to about 7 log fold, each inclusive, compared to a reference expression level of MFI2. In particular embodiments, the change in expression level is about 1 log fold to about 7 log fold. In specific embodiments, the selectedgene is MFI2 and MFI2 is downregulated by about a change in expression level of about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, about 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, or about 7 log fold, compared to a reference expression level of MFI2. In particular embodiments, the change in expression level is about 2.3 log fold. In particular embodiments, the change in expression level is about 4.7 log fold.

[0152] In specific embodiments, the selected gene is IPO 13 and IPO 13 is downregulated by a change in expression level of about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of IPO 13. In particular embodiments, the change in expression level is about 1 log fold to about 5 log fold. In specific embodiments, the selected gene is IPO 13 and IPO 13 is downregulated by about a change in expression level of about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of IPO13. In particular embodiments, the change in expression level is about 2.3 log fold. In particular embodiments, the change in expression level is about 2.4 log fold.

[0153] In specific embodiments, the selected gene is ARHGEF28 and ARHGEF28 is downregulated by a change in expression level of about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of ARHGEF28. In particular embodiments, the change in expression level is about 1 log fold to about 5 log fold. In specific embodiments, the selected gene is ARHGEF28 and ARHGEF28 is downregulated by about a change in expression level of about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about4.5 log fold, or about 5.0 log fold, compared to a reference expression level of ARHGEF28. In particular embodiments, the change in expression level is about 2.3 log fold. In particular embodiments, the change in expression level is about 2.2 log fold.

[0154] In specific embodiments, the selected gene is ATP2A1 and ATP2A1 is downregulated by a change in expression level of about 1 log fold to about 7 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, about 3 log fold to about 7 log fold, about 3 log fold to about 5 log fold, or about 5 log fold to about 7 log fold, eachinclusive, compared to a reference expression level of ATP2A1. In particular embodiments, the change in expression level is about 1 log fold to about 7 log fold. In specific embodiments, the selected gene is ATP2A1 and ATP2A1 is downregulated by about a change in expression level of about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, about 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, or about 7 log fold, compared to a reference expression level of ATP2A1. In particular embodiments, the change in expression level is about 2.2 log fold. In particular embodiments, the change in expression level is about 4.8 log fold.

[0155] In specific embodiments, the selected gene is SORBS2 and SORBS2 is downregulated by a change in expression level of about 1 log fold to about 7 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, about 3 log fold to about 7 log fold, about 3 log fold to about 5 log fold, or about 5 log fold to about 7 log fold, each inclusive, compared to a reference expression level of SORBS2. In particular embodiments, the change in expression level is about 1 log fold to about 7 log fold. In specific embodiments, the selected gene is SORBS2 and SORBS2 is downregulated by about a change in expression level of about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, about 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, or about 7 log fold, compared to a reference expression level of SORBS2. In particular embodiments, the change in expression level is about 2.1 log fold. In particular embodiments, the change in expression level is about 5.0 log fold.

[0156] In specific embodiments, the selected gene is AD API and AD API is downregulated by a change in expression level of about 1 log fold to about 7 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, about 3 log fold to about 7 log fold, about 3 log fold to about 5 log fold, or about 5 log fold to about 7 log fold, each inclusive, compared to a reference expression level of AD API. In particular embodiments, the change in expression level is about 1 log fold to about 7 log fold. In specific embodiments, the selected gene is AD API and AD API is downregulated by about a change in expression level of about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, about 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, or about 7 log fold, compared to a reference expression level of AD API. In particular embodiments, the change in expression level isabout 1.9 log fold. In particular embodiments, the change in expression level is about 4.0 log fold.

[0157] In specific embodiments, the selected gene is TLE3 and TLE3 is downregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of TLE3. In particular embodiments, the change in expression level is about 0.5 log fold to about 3.0 log fold. In specific embodiments, the selected gene is TLE3 and TLE3 is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 log fold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of TLE3. In particular embodiments, the change in expression level is about 1.8 log fold. In particular embodiments, the change in expression level is about 1.0 log fold.

[0158] In specific embodiments, the selected gene is Cl lorf54 and Cl lorf54 is downregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of Cl lorf54. In particular embodiments, the change in expression level is about 0.5 log fold to about 3.0 log fold. In specific embodiments, the selected gene is Cl lorf54 and Cl lorf54 is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 log fold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of TLE3. In particular embodiments, the change in expression level is about 1.7 log fold. In particular embodiments, the change in expression level is about 1.0 log fold.

[0159] In specific embodiments, the selected gene is CD58 and CD58 is downregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold,about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of CD58. In particular embodiments, the change in expression level is about 0.5 log fold to about 3.0 log fold. In specific embodiments, the selected gene is CD58 and CD58 is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 log fold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of CD58. In particular embodiments, the change in expression level is about 1.7 log fold. In particular embodiments, the change in expression level is about 1.5 log fold.

[0160] In specific embodiments, the selected gene is MOG and MOG is downregulated by a change in expression level of about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of MOG. In particular embodiments, the change in expression level is about 1 log fold to about 5 log fold. In specific embodiments, the selected gene is MOG and MOG is downregulated by about a change in expression level of about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of MOG. In particular embodiments, the change in expression level is about 1.6 log fold. In particular embodiments, the change in expression level is about 2.7 log fold.

[0161] In specific embodiments, the selected gene is DYPSL5 and DYPSL5 is downregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of DYPSL5. In particular embodiments, the change in expression level is about 0.5 log fold to about 3.0 log fold. In specific embodiments, the selected gene is DYPSL5 and DYPSL5 is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 log fold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of DYPSL5. In particular embodiments, the change in expression level is about 1.5 log fold. In particular embodiments, the change in expression level is about 1.2 log fold.

[0162] In specific embodiments, the selected gene is HNRNPL and HNRNPL is downregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of HNRNPL. In particular embodiments, the change in expression level is about 0.5 log fold to about 3.0 log fold. In specific embodiments, the selected gene is HNRNPL and HNRNPL is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 log fold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of HNRNPL. In particular embodiments, the change in expression level is about 1.5 log fold.

[0163] In specific embodiments, the selected gene is PDIA3 and PDIA3 is downregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of PDIA3. In particular embodiments, the change in expression level is about 0.5 log fold to about 3.0 log fold. In specific embodiments, the selected gene is PDIA3 and PDIA3 is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 log fold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of PDIA3. In particular embodiments, the change in expression level is about 1.2 log fold. In particular embodiments, the change in expression level is about 1.3 log fold.

[0164] In specific embodiments, the selected gene is PLXNB3 and PLXNB3 is downregulated by a change in expression level of about 0.5 log fold to about 5 log fold, about 0.5 log fold to about 3 log fold, about 0.5 log fold to about 1 log fold, about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of PLXNB3. In particular embodiments, the change in expression level is about 0.5 log fold to about 3.0 log fold. In specific embodiments, the selected gene is PLXNB3 and PLXNB3 is upregulated by about a change in expression level of about 0.5 log fold, about 0.6 log fold, about 0.7 log fold, about 0.8 log fold, about 0.9 log fold, about 1.0 log fold, about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of PLXNB3. In particular embodiments, the change in expression level is about 1.1 log fold. In particular embodiments, the change in expression level is about 1.0 log fold.

[0165] In specific embodiments, the selected gene is HUNK and HUNK is downregulated by a change in expression level of about 1 log fold to about 5 log fold, about 1 log fold to about 3 log fold, or about 3 log fold to about 5 log fold, each inclusive, compared to a reference expression level of HUNK. In particular embodiments, the change in expression level is about 1 log fold to about 5 log fold. In specific embodiments, the selected gene is HUNK and HUNK is downregulated by about a change in expression level of about 1.1 log fold, about 1.2 log fold, about 1.3 log fold, about 1.4 log fold, about 1.5 log fold, about 1.6 log fold, about 1.7 log fold, about 1.8 log fold, about 1.9 log fold, about 2.0 log fold, about 2.5 log fold, about 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, or about 5.0 log fold, compared to a reference expression level of HUNK. In particular embodiments, the change in expression level is about 1.0 log fold. In particular embodiments, the change in expression level is about 2.3 log fold.

[0166] In certain embodiments, the altered expression profile comprises a change to a gene, a transcript, or a protein selected from the group consisting of HEY1, IFI27L2, ARHGAP6, SPON2, SCUBE3, MYLPF, LFNG, HSD3B7, TMEM200B, ABAT, KCTD12, GSTM3, TNNI3, SEMA3E, HES1, UCP2, GALNT15, ADPRHL1, MARCKSL1, RAB11FIP1, AN08, NTN1, SKAP2, GPT, COX7A2, DKK1, GPD1, BAIAP2, RABEPK, SHD, CEMIP, XYLT1, CPAMD8, PSMB8, FBP1, DLL1, MFI2, TLCD1, IPO13, ANKRD24, GALNT3, ARHGEF28, BCL2L13, THRAP3, SCARA5, MTTP, RANGRF,ATP2A1, WDR83, S0RBS2, ASL, PSMB10, SLC12A8, TM7SF2, AD API, ANXA3, LAMA3, TLE3, FREM2, FAM60A, C11ORF54, MYO16, CD58, ZEB2, STAC3, HYAL2, EMD, CDH2, CRAT, MEI, PLA2G6, LGALS9, DOK7, MOG, HIST1H1E, FRAT2, SLC35D1, BAG2, HNRNPL, C14ORF159, SLC45A3, FMN2, STAC2, TTC28, SLC38A5, PTPRE, LSS, AMOTL2, CACNA1H, GPC5, SLC9A3R1, TPGS1, ARPP21, PLEKHG1, TUBA1A, EIF2AK2, MURC, JPH1, PPP2R3B, BPGM, ARHGAP8, TPCN2, PDIA3, ARSI, IER2, PLXNB3, SPG20, TMEM198B, HUNK, HGD, ALAS1, TGM1, and a combination thereof.

[0167] In certain embodiments, the change to the selected gene, transcript, or protein comprises a genetic variant comprising an intragenic or an intron variant. In specific embodiments, the genetic variant comprises an intragenic variant. In specific embodiments, the genetic variant comprises an intron variant. In specific embodiments, the non-deleterious effect comprises an alteration or a change in effectiveness of the resulting protein. In particular embodiments, the effectiveness of the resulting protein is decreased. In particular embodiments, the effectiveness of the resulting protein is increased.

[0168] In certain embodiments, the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is downregulated by a change of about 0.5 to about 14 log fold, about 0.5 to about 12 log fold, 0.5 to about 10 log fold, about 0.5 to about 8 log fold, about 0.5 to about 6 log fold, about 0.5 to about 4 log fold, or about 0.5 to about 2 log fold, each inclusive, compared to a reference expression level of the selected gene. In certain embodiments, the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is downregulated by a change of about 1.0 log fold, about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, 7.0 log fold, about 7.5 log fold, about 8.0 log fold, about 8.5 log fold, about 9.0 log fold, about 9.5 log fold, or about 10.0 log fold, compared to a reference expression level of the selected gene.

[0169] In some embodiments, the reference expression level is the expression level of the same gene, transcript, or protein in a non-altered cell line. In some embodiments, the reference expression level is the expression level of the same gene, transcript, or protein in a corresponding adherent cell line. In some embodiments, the reference expression level is the expression level of the same gene, transcript, or protein in a reference adherent line. In some embodiments, the non-altered cell line can be the parent cell line from which the altered cell line is derived from. In some embodiments, the corresponding adherent cell line can be theparent adherent cell line from which the non-adherent cell line, e.g., suspension cell line, is derived from. In some embodiments, the reference adherent cell line can be the parent adherent cell line from which the non-adherent cell line, e.g., suspension cell line, is derived from. In some embodiments, the reference expression level is a mean expression level of multiple non-altered, corresponding adherent, and / or reference adherent cell lines. In some embodiments, the reference expression level is a mean expression level of multiple nonaltered, corresponding adherent, and / or reference adherent cell lines.

[0170] One of skill in the art will understand how to define a reference expression level for a specific gene, transcript, or protein and to define upregulation and / or downregulation in terms of gene expression for that specific gene, transcript, or protein as a matter of routine skill. The reference expression level may be defined according to specific parameters of, for example, but not limited to, the assay or method of sequencing, the identity of the specific gene, transcript, or protein, reagents used, and / or instrumentation used. One of skill in the art will also understand how to decide on a proper reference genome and how to determine genetic variance for a specific gene, transcript, or protein as a matter of routine skill. Choosing the reference genome may take into consideration, for example, but not limited to, the cell line to be used, the culturing conditions, the assay or method of sequencing, the identity of the specific gene, transcript, or protein, reagents used, and / or instrumentation used.Additional Embodiments of the Present Disclosure

[0171] Disclosed herein are altered cell lines and methods for generating and maintaining the altered cells. The altered cell lines preferably comprise BFT cells. The altered cell lines have been adapted to serum- free suspension culture without the use of microcarriers. The altered cell lines are further cultured in the presence of a medium as described herein.

[0172] In one embodiment, the disclosure relates to a composition comprising altered cell lines that have an altered expression profile as compared to an expression profile of a corresponding non-altered cell line. The altered cell line can be a suspension cell line or an adherent cell line.

[0173] In another embodiment, the disclosure relates to a method for generating an altered cell line, the method comprising providing an adherent cell line or derivative thereof to a process sufficient to generate an altered expression profile that is different than an expression profile of a corresponding non-altered cell line.

[0174] In some embodiments, the altered cell lines have an average doubling time of between about 10 hours and about 200 hours (e.g., between about 12 hours and about 200 hours). In some embodiments, the altered cell lines have an average doubling time of between about 16 hours and about 60 hours.

[0175] In some embodiments, the altered cell line is a suspension cell line. The suspension cell line can be stable in growth (e.g. growth rate, cell density, reduced doubling time), morphology (e.g. cell size) and response (e.g. altered gene expression of a target gene compared to an adherent cell line from which the suspension cell line was derived). The suspension cell line can be grown in shaker vessels such as filter tubes, single-use or stainless steel bioreactors and / or stirred tank vessels for bulk cell production.

[0176] In some embodiments, the altered cell line can be derived from an aquatic animal, in particular, from any fish, mollusk and crustacean, using any suitable methods. In another embodiment, the fish can be one or more of a cartilaginous fish, bony fish, ray-finned fish, lobe-finned fish, mollusks, mussels, cephalopods, crustaceans, and echinoderms.

[0177] In some embodiments, the altered cell line may be derived from an aquatic species of at least one species selected from the group consisting of Bluefin tuna (Thunnus orientalis, Thunnus maccoyii, and Thunnus thynnus), yellowfin tuna (Thunnus albacares), yellowtail (e.g., Seriola lalandi), mahi-mahi (Coryphaena hippurus), red snapper (Lutjanus campechanus). cod (e.g., Gadus morhua, Gadus Macrocephalus, Gadus ogac), flounder, halibut, herring, mackeral, pompano, salmon (Salmo salar), sea bass, Patagonian toothfish (Dissostichus eleginoides), squid, clams, lobster, crabs, scallops, shrimp, eel, bass (e.g., Micropterus salmoides), bluegill (Lepomis macrochirus), rainbow trout (Oncorhynchus rnykiss), tilapia (Oreochromis massambicus), and carp (e.g., Hypophthalmichthys molitrix).

[0178] In another embodiment the altered cell line composition is derived from an aquatic animal species comprising at least one species selected from the group consisting of one of the eight species of tunas in the genus Thunnus. These include the northern Bluefin tuna (T. thynnus ), albacore (T. alalunga), yellowfin tuna (T. albacares), southern Bluefin tuna (T. thynnus maccoyii), bigeye tuna (T. obesus), blackfin tuna (T. atlanticus), Pacific Bluefin tuna (T. orientalis) and longtail tuna (T. tonggol). See https: / / www.britannica.com / animal / tuna- fish, which is incorporated by reference herein.

[0179] In addition to altered cell lines derived from the genus Thunnus, particularly Bluefin tuna cells, cells from a wide variety of fish species can be used. Such species include but are not limited to bass, flounder, hake, scup, smelt, rainbow trout, hardshell clam, blue crab, peekytoe crab, spanner crab, cuttlefish, Eastern oyster, Pacific oyster, anchovy, herring,lingcod, moi, orange roughy, Atlantic Ocean perch, Lake Victoria perch, yellow perch, European oyster, Dover sole, sturgeon, tilefish, wahoo, yellowtail, sea urchin, Atlantic mackerel, sardines, black sea bass, European sea bass, hybrid striped bass, bream, cod, drum, haddock, hoki, Alaska pollock, rockfish, pink salmon, snapper, tilapia, turbot, walleye, lake whitefish, wolffish, hardshell clam, surf clam, cockle, Jonah crab, snow crab, crayfish, bay scallop, Chinese white shrimp, sablefish, Atlantic salmon, coho salmon, skate, dungeness crab, king crab, blue mussel, greenshell mussel, pink shrimp, Escolar, chinook salmon, chum salmon, American shad, Arctic char, carp, catfish, dory, grouper, halibut, monkfish, pompano, abalone, conch, stone crab, American lobster, spiny lobster, octopus, black tiger shrimp, freshwater shrimp, gulf shrimp, Pacific white shrimp, squid, barramundi, cusk, dogfish, kingklip, mahi-mahi, opah, mako shark, swordfish, albacore tuna, yellowfin tuna, geoduck clam, squat lobster, sea scallop, rock shrimp, barracuda, Chilean sea bass, cobia, croaker, eel, blue marlin, mullet, sockeye salmon, Bluefin tuna, shrimp, crabs, lobster, and echinoderms (e.g. sea cucumbers and sea urchins).

[0180] In some embodiments, the altered cell line can be derived from myoblasts, myocytes, adipocytes, fibroblasts, keratinocytes, epithelial cells, endothelial cells, embryonic derived cells, induced pluripotent stem cells, or mesenchymal stem cells. In another embodiment, the cell can be one or more of myoblasts, myocytes, preadipocytes, adipocytes, fibroblasts, keratinocytes, epithelial cells, endothelial cells, embryonic derived cells, induced pluripotent stem cells, mesenchymal stem cells, and combinations thereof of the animal. In one embodiment, the cell can be one or more of myoblasts, preadipocytes, and fibroblasts. In another embodiment, the cell line can be selected from the group of preadipocyte lines, myoblast lines and fibroblasts lines.

[0181] In some embodiments, the altered cell line can have an altered expression profile as compared to an expression profile of a corresponding non-altered cell line. In some embodiments, the altered expression profile can be an upregulated gene expression profile. In some embodiments, the altered expression profile can be a downregulated gene expression profile.

[0182] In some embodiments, the altered cell line may have an altered expression profile that can be a gene, a transcript, or a protein selected from the group consisting of ABCG2, SI, NDUFS8, ITGA5, CNTD1, PKHD1L1, PLXNB2, CASP10, FN1, ASAP2, IL13RA2, DAAM2, MCTP1, NUGGC, MEGF10, KIAA1324L, CPXM1, PHACTR4, FGF13, FLT1, PRICKLEI, ZEB1, SULF2, NET1, KIFAP3, HDAC9, DOPEY2, MAN2B2, TLE4, GARNL3, PFKP, ANKS1B, ABHD4, GTPBP2, PLXNA3, CREB3, NLRP12, PTPRK,RGN, GLUL, ABCG2, SI, MMP13, CMYA5, CAMTAI, ABCA1, CDH1, NDUFS8, EPHA10, DCHS1, OLFML1, ITGA5, SLC12A5, F8, CNTD1, PKHD1L1, ARHGAP22, LTBP3, PPP1R42, ADH5, REEP1, ADAMTS1, ATF5, ALDH1L1, ADAMTSL3, PLXNB2, CASP1O, CSF1R, BSCL2, SLC15A2, CYP3A4, FN1, KIAA1644, ABCC6, GARS, ANTXRL, ASAP2, GGT7, GARS, P2RY4, ABCA1, IL1B, PRKAG2, TNFAIP3, VASP, FSTL1, IL13RA2, KLHL38, SLC47A2, SLC5A5, FKBP14, MAGI2, GTPBP1, DAAM2, EXOC3L1, RAB37, KRT12, SLCO2B1, ADM2, MCTP1, DACT2, NUGGC, CHRD, ROBO3, MMP19, PTK7, PLEKHH1, MEGF10, FERMT1, SRPX2, TOX3, CTSS, MST1R, CCDC108, SEMA6C, AVPR1A, TSC22D4, FSTL3, ITGA2, PTGIS, COLEC12, KIAA1324L, NLN, FBXO32, CCDC153, CPXM1, PHACTR4, FGF13, DOCKIO, CYSTM1, FAM214A, CAND2, ARHGEF25, PTPLAD2, PAMR1, ULK2, PRODH, KRT8, TRIM55, KIAA1522, OPLAH, PREXI, LRP2, TBC1D2, INVS, FLT1, PRICKLEI, ADAMTS12, MDM2, CSRNP1, RTP4, MED13L, NFKBIA, RGS12, LMNA, RIN1, TCN2, PDE7B, COL23A1, KIAA0141, ANTXRL, AATK, ZEB1, IL1RAP, COL23A1, SULF2, MXRA8, ZMIZ1, TMTC2, KIFAP3, ISG15, MAP6, HDAC9, ACSL3, DOPEY2, MAN2B2, GARNL3, MKL2, ATXN1, WDFY2, CAPN2, ERRFI1, FARP1, HFE2, ZC3H12D, PFKP, ANKS1B, UAP1L1, ABHD4, RNF165, MPP5, SAT1, HBP1, AMPD2, HOMEZ, B3GNT2, GTPBP2, STEAP4, PCDHAC2, COL4A3BP, TNS3, RNF169, AEBP1, TFE3, TTYH1, NEIL1, KIAA1033, MMP14, ACSL4, KLHL40, LPIN1, FGD1, XPC, PLXNA3, TNFAIP2, CCDC92, DAB2, MTMR11, ZFYVE28, PC, ADIPOR2, MYODI, ZBTB33, METRNL, TBC1D2B, MFAP5, SCD, PPP1R3C, VPS4B, QPCT, METRNL, CTSH, CREB3, ARHGAP24, WDFY4, ROR2, ATP6V1B2, CTSZ, CXADR, MFSD2A, AVIL, XKRX, NLRP12, PTPRK, CHRNG, TIFA, TMCC3, SEMA4B, GDF10, PARD3, RGN, MAN2B1, PNPLA6, COL15A1, VPS41, TBC1D26, GHDC, ATHL1, NUGGC, TBC1D26, FSTL3, PNPLA6, XKRX, LTBP3, MFAP5, ABCC6, CSF1R, FARP1, SRPX2, LRP2, AATK, KRT12, MCTP1, CCDC153, SLC5A5, KRT8, PAMR1, FN1, HEY1, SCUBE3, MYLPF, MARCKSL1, RAB11FIP1, NTN1, GPT, GPD1, BAIAP2, MFI2, IPO13, ARHGEF28, ATP2A1, SORBS2, AD API, TLE3, C11ORF54, CD58, MOG, DPYS15, HNRNPL, PDIA3, PLXNB3, HUNK, HEY1, MYLPF, SCUBE3, SORBS2, ATP2A1, MFI2, BAIAP2, AD API, RAB11FIP1, MARCKSL1, MOG, IPO13, HUNK, ARHGEF28, NTN1, GPD1, GPT, CD58, HNRNPL, PDIA3, DPYS15, TLE3, C11ORF54, PLXNB3, HEY1, IFI27L2, ARHGAP6, SPON2, SCUBE3, MYLPF, LFNG, HSD3B7, TMEM200B, ABAT, KCTD12, GSTM3, TNNI3, SEMA3E, HES1, UCP2, GALNT15, ADPRHL1, MARCKSL1, RAB11FIP1, ANO8, NTN1, SKAP2, GPT, COX7A2, DKK1, GPD1, BAIAP2, RABEPK, SHD, CEMIP,XYLT1, CPAMD8, PSMB8, FBP1, DLL1, MFI2, TLCD1, IP013, ANKRD24, GALNT3, ARHGEF28, BCL2L13, THRAP3, SCARA5, MTTP, RANGRF, ATP2A1, WDR83, S0RBS2, ASL, PSMB10, SLC12A8, TM7SF2, AD API, ANXA3, LAMA3, TLE3, FREM2, FAM60A, C11ORF54, MYO16, CD58, ZEB2, STAC3, HYAL2, EMD, CDH2, CRAT, MEI, PLA2G6, LGALS9, DOK7, MOG, HIST1H1E, FRAT2, SLC35D1, BAG2, HNRNPL, C14ORF159, SLC45A3, FMN2, STAC2, TTC28, SLC38A5, PTPRE, LSS, AMOTL2, CACNA1H, GPC5, SLC9A3R1, TPGS1, ARPP21, PLEKHG1, TUBA1A, EIF2AK2, MURC, JPH1, PPP2R3B, BPGM, ARHGAP8, TPCN2, PDIA3, ARSI, IER2, PLXNB3, SPG20, TMEM198B, HUNK, HGD, ALAS1, IFI27L2, ANO8, HEY1V MYLPF, UCP2, ABAT, SCUBE3, ANKRD24, ZEB2, ARHGAP6, SORBS2, ATP2A1, ADPRHL1, MFI2, HES1, BAIAP2, TNNI3, HIST1H1E, TMEM200B, AD API, SEMA3E, MURC, ALAS1, RAB11FIP1, TTC28, CRAT, MARCKSL1, IER2, MOG, XYLT1, SLC45A3, HSD3B7, IPO13, HYAL2, HUNK, FBP1, ARHGEF28, EMD, AMOTL2, MYO16, GALNT15, GPD1, TGM1, CPAMD8, THRAP3, LAMA3, C14ORF159, FREM2, STAC2, GSTM3, JPH1, SHD, HGD, GPC5, DOK7, STAC3, BCL2L13, KCTD12, BPGM, TUBA1A, GALNT3, GPT, HNRNPL, DKK1, PLEKHG1, ARHGAP8, CEMIP, WDR83, NTN1, MEI, BAG2, CACNA1H, RABEPK, SLC9A3R1, TPCN2, PDIA3, LGALS9, RANGRF, LSS, PPP2R3B, SPG20, TM7SF2, EIF2AK2, PSMB8, SLC38A5, TLCD1, FRAT2, SKAP2, CDH2, ASL, FMN2, ARPP21, TPGS1, FAM60A, PLA2G6, PSMB10, COX7A2, SCARA5, DLL1, TLE3, LFNG, MTTP, TMEM198B, PLXNB3, SPON2, ANXA3, SLC35D1, C11ORF54, PTPRE, and a combination thereof.

[0183] In some embodiments, the gene, transcript, or protein is selected from the group consisting of ABCG2, SI, NDUFS8, ITGA5, CNTD1, PKHD1L1, PLXNB2, CASP10, FN1, ASAP2, IL13RA2, DAAM2, MCTP1, NUGGC, MEGF10, KIAA1324L, CPXM1, PHACTR4, FGF13, FLT1, PRICKLEI, ZEB1, SULF2, NET1, KIFAP3, HDAC9, DOPEY2, MAN2B2, TLE4, GARNL3, PFKP, ANKS1B, ABHD4, GTPBP2, PLXNA3, CREB3, NLRP12, PTPRK, RGN, and a combination thereof.

[0184] In some embodiments, the gene, transcript, or protein is selected from the group consisting of GLUL, ABCG2, SI, MMP13, CMYA5, CAMTAI, ABCA1, CDH1, NDUFS8, EPHA10, DCHS1, OLFML1, ITGA5, SLC12A5, F8, CNTD1, PKHD1L1, ARHGAP22, LTBP3, PPP1R42, ADH5, REEP1, ADAMTS1, ATF5, ALDH1L1, ADAMTSL3, PLXNB2, CASP10, CSF1R, BSCL2, SLC15A2, CYP3A4, FN1, KIAA1644, ABCC6, GARS, ANTXRL, ASAP2, GGT7, GARS, P2RY4, ABCA1, IL1B, PRKAG2, TNFAIP3, VASP, FSTL1, IL13RA2, KLHL38, SLC47A2, SLC5A5, FKBP14, MAGI2, GTPBP1, DAAM2,EX0C3L1, RAB37, KRT12, SLC02B1, ADM2, MCTP1, DACT2, NUGGC, CHRD, R0B03, MMP19, PTK7, PLEKHH1, MEGF10, FERMT1, SRPX2, TOX3, CTSS, MST1R, CCDC1O8, SEMA6C, AVPR1A, TSC22D4, FSTL3, ITGA2, PTGIS, COLEC12, KIAA1324L, NLN, FBXO32, CCDC153, CPXM1, PHACTR4, FGF13, DOCKIO, CYSTM1, FAM214A, CAND2, ARHGEF25, PTPLAD2, PAMR1, ULK2, PRODH, KRT8, TRIM55, KIAA1522, OPLAH, PREXI, LRP2, TBC1D2, INVS, FLT1, PRICKLEI, ADAMTS12, MDM2, CSRNP1, RTP4, MED13L, NFKBIA, RGS12, LMNA, RIN1, TCN2, PDE7B, COL23A1, KIAA0141, ANTXRL, AATK, ZEB1, IL1RAP, COL23A1, SULF2, MXRA8, ZMIZ1, TMTC2, KIFAP3, ISG15, MAP6, HDAC9, ACSL3, DOPEY2, MAN2B2, GARNL3, MKL2, ATXN1, WDFY2, CAPN2, ERRFI1, FARP1, HFE2, ZC3H12D, PFKP, ANKS1B, UAP1L1, ABHD4, RNF165, MPP5, SAT1, HBP1, AMPD2, HOMEZ, B3GNT2, GTPBP2, STEAP4, PCDHAC2, COL4A3BP, TNS3, RNF169, AEBP1, TFE3, TTYH1, NEIL1, KIAA1033, MMP14, ACSL4, KLHL40, LPIN1, FGD1, XPC, PLXNA3, TNFAIP2, CCDC92, DAB2, MTMR11, ZFYVE28, PC, ADIPOR2, MYODI, ZBTB33, METRNL, TBC1D2B, MFAP5, SCD, PPP1R3C, VPS4B, QPCT, METRNL, CTSH, CREB3, ARHGAP24, WDFY4, ROR2, ATP6V1B2, CTSZ, CXADR, MFSD2A, AVIL, XKRX, NLRP12, PTPRK, CHRNG, TIFA, TMCC3, SEMA4B, GDF10, PARD3, RGN, MAN2B1, PNPLA6, COL15A1, VPS41, TBC1D26, GHDC, ATHL1, NUGGC, TBC1D26, FSTL3, PNPLA6, XKRX, LTBP3, MFAP5, ABCC6, CSF1R, FARP1, SRPX2, LRP2, AATK, KRT12, MCTP1, CCDC153, SLC5A5, KRT8, PAMR1, FN1, and a combination thereof.

[0185] In some embodiments, the gene, transcript or protein is selected from the group consisting of HEY1, SCUBE3, MYLPF, MARCKSL1, RAB11FIP1, NTN1, GPT, GPD1, BAIAP2, MFI2, IPO13, ARHGEF28, ATP2A1, SORBS2, AD API, TLE3, C11ORF54, CD58, MOG, DPYS15, HNRNPL, PDIA3, PLXNB3, HUNK, HEY1, MYLPF, SCUBE3, SORBS2, ATP2A1, MFI2, BAIAP2, AD API, RAB11FIP1, MARCKSL1, MOG, IPO13, HUNK, ARHGEF28, NTN1, GPD1, GPT, CD58, HNRNPL, PDIA3, DPYS15, TLE3, C11ORF54, PLXNB3, and a combination thereof.

[0186] In some embodiments, the altered cell line composition comprises a gene, a transcript, or a protein selected from the group consisting of HEY1, IFI27L2, ARHGAP6, SPON2, SCUBE3, MYLPF, LFNG, HSD3B7, TMEM200B, ABAT, KCTD12, GSTM3, TNNI3, SEMA3E, HES1, UCP2, GALNT15, ADPRHL1, MARCKSL1, RAB11FIP1, ANO8, NTN1, SKAP2, GPT, COX7A2, DKK1, GPD1, BAIAP2, RABEPK, SHD, CEMIP, XYLT1, CPAMD8, PSMB8, FBP1, DLL1, MFI2, TLCD1, IPO13, ANKRD24, GALNT3, ARHGEF28, BCL2L13, THRAP3, SCARA5, MTTP, RANGRF, ATP2A1, WDR83,S0RBS2, ASL, PSMB10, SLC12A8, TM7SF2, AD API, ANXA3, LAMA3, TLE3, FREM2, FAM60A, C11ORF54, MYO16, CD58, ZEB2, STAC3, HYAL2, EMD, CDH2, CRAT, MEI, PLA2G6, LGALS9, DOK7, MOG, HIST1H1E, FRAT2, SLC35D1, BAG2, HNRNPL, C14ORF159, SLC45A3, FMN2, STAC2, TTC28, SLC38A5, PTPRE, LSS, AMOTL2, CACNA1H, GPC5, SLC9A3R1, TPGS1, ARPP21, PLEKHG1, TUBA1A, EIF2AK2, MURC, JPH1, PPP2R3B, BPGM, ARHGAP8, TPCN2, PDIA3, ARSI, IER2, PLXNB3, SPG20, TMEM198B, HUNK, HGD, ALAS1, IFI27L2, ANO8, HEY1V MYLPF, UCP2, ABAT, SCUBE3, ANKRD24, ZEB2, ARHGAP6, SORBS2, ATP2A1, ADPRHL1, MFI2, HES1, BAIAP2, TNNI3, HIST1H1E, TMEM200B, AD API, SEMA3E, MURC, ALAS1, RAB11FIP1, TTC28, CRAT, MARCKSL1, IER2, MOG, XYLT1, SLC45A3, HSD3B7, IPO13, HYAL2, HUNK, FBP1, ARHGEF28, EMD, AMOTL2, MYO16, GALNT15, GPD1, TGM1, CPAMD8, THRAP3, LAMA3, C14ORF159, FREM2, STAC2, GSTM3, JPH1, SHD, HGD, GPC5, DOK7, STAC3, BCL2L13, KCTD12, BPGM, TUBA1A, GALNT3, GPT, HNRNPL, DKK1, PLEKHG1, ARHGAP8, CEMIP, WDR83, NTN1, MEI, BAG2, CACNA1H, RABEPK, SLC9A3R1, TPCN2, PDIA3, LGALS9, RANGRF, LSS, PPP2R3B, SPG20, TM7SF2, EIF2AK2, PSMB8, SLC38A5, TLCD1, FRAT2, SKAP2, CDH2, ASL, FMN2, ARPP21, TPGS1, FAM60A, PLA2G6, PSMB10, COX7A2, SCARA5, DLL1, TLE3, LFNG, MTTP, TMEM198B, PLXNB3, SPON2, ANXA3, SLC35D1, C11ORF54, PTPRE, and a combination thereof.

[0187] In one embodiment, the present disclosure provides a method for generating a method for generating an altered cell line, the method comprising (a) providing an adherent cell line or derivative thereof; and (b) subjecting said adherent cell line or derivative thereof to a process sufficient to generate an altered expression profile that is different than an expression profile of a corresponding non-altered cell line. In some embodiments, the method generates an altered cell line that is a suspension cell line. In some embodiments, the method generates an altered cell line that is an adherent cell line.

[0188] In some embodiments, the method generates an altered cell line that is derived from an aquatic species. In some embodiments, the method generates an altered cell line from an aquatic species comprising at least one species selected from the group consisting of Bluefin tuna (Thunnus orientalis, Thunnus maccoyii, and Thunnus thynnus), yellowfin tuna (Thunnus albacares), yellowtail (e.g., Seriola lalandi), mahi-mahi {Coryphaena hippurus), red snapper (Lutjanus campechanus), cod (e.g., Gadus morhua, Gadus Macrocephalus, Gadus ogac), flounder, halibut, herring, mackeral, pompano, salmon (Salmo salar), sea bass, Patagonian toothfish (Dissostichus eleginoides), squid, clams, lobster, crabs, scallops, shrimp,eel, bass (e.g., Micropterus salmoides), bluegill (Lepomis macrochirus), rainbow trout (Oncorhynchus mykiss), tilapia (Oreochromis massambicus), and carp (e.g., Hypophthalmichthys molilrix).

[0189] In another embodiment the method generates an altered cell that is derived from an aquatic species comprising at least one species selected from the group consisting of the eight species of tunas in the genus Thunnus. These include the Bluefin tuna (T. thynnus), albacore (T. alalunga), yellowfin tuna (T. albacares'), southern Bluefin tuna (T. thynnus maccoyii), bigeye tuna (T. obesus), blackfin tuna (T. atlanticus), Pacific Bluefin tuna (Thunnus orienlalis), and longtail tuna (T. tonggol). See https: / / www.britannica.com / animal / tuna-fish, which is incorporated by reference herein.

[0190] In another embodiment, in addition to altered tuna cell lines derived from the genus Thunnus, particularly Bluefin tuna cells, the method generates altered cell lines from a wide variety of fish species. Such species include but are not limited to bass, flounder, hake, scup, smelt, rainbow trout, hardshell clam, blue crab, peekytoe crab, spanner crab, cuttlefish, Eastern oyster, Pacific oyster, anchovy, herring, lingcod, moi, orange roughy, Atlantic Ocean perch, Lake Victoria perch, yellow perch, European oyster, Dover sole, sturgeon, tilefish, wahoo, yellowtail, sea urchin, Atlantic mackerel, sardines, black sea bass, European sea bass, hybrid striped bass, bream, cod, drum, haddock, hoki, Alaska pollock, rockfish, pink salmon, snapper, tilapia, turbot, walleye, lake whitefish, wolffish, hardshell clam, surf clam, cockle, Jonah crab, snow crab, crayfish, bay scallop, Chinese white shrimp, sablefish, Atlantic salmon, coho salmon, skate, dungeness crab, king crab, blue mussel, greenshell mussel, pink shrimp, Escolar, chinook salmon, chum salmon, American shad, Arctic char, carp, catfish, dory, grouper, halibut, monkfish, pompano, abalone, conch, stone crab, American lobster, spiny lobster, octopus, black tiger shrimp, freshwater shrimp, gulf shrimp, Pacific white shrimp, squid, barramundi, cusk, dogfish, kingklip, mahi-mahi, opah, mako shark, swordfish, albacore tuna, yellowfin tuna, geoduck clam, squat lobster, sea scallop, rock shrimp, barracuda, Chilean sea bass, cobia, croaker, eel, blue marlin, mullet, sockeye salmon, Bluefin tuna, shrimp, crabs, lobster, and echinoderms (e.g. sea cucumbers and sea urchins).

[0191] In some embodiments, the method for generating an altered cell line comprises contacting the adherent cell line with a chemical mutagen, a physical mutagen, electromagnetic radiation, particle radiation, a virus, or combinations thereof. In some embodiments, the chemical mutagen is selected from a group consisting of alkylating agents, azides, and a combination thereof. In some embodiments, the particle radiation is selected from the group consisting of fast neutrons, thermal neutrons, beta particles, alpha particles,and combinations thereof. In some embodiments, the electromagnetic radiation is selected from the group consisting of gamma ray, x-rays, UV light, and combinations thereof.

[0192] In some embodiments, the method for generating an altered cell line comprises contacting an adherent cell line with a heterologous gene including a gene regulating moiety, wherein said gene regulating moiety is configured to regulate an expression of a target gene, a target transcript, or a target protein of the adherent cell line or derivative thereof, thereby effecting a modified expression profile of the target gene, the transcript, or the target protein in the altered suspension cell line as compared to the corresponding non-altered cell line. In some embodiments, the gene regulating moiety is an endonuclease. In some embodiments, the endonuclease is a clustered regularly interspaced short palindromic repeats (CRISPR)- associated (CAS) endonuclease.

[0193] In some embodiments, the heterologous gene including a gene regulating moiety is delivered to the adherent cell line by recombinant DNA or RNA vector construct. As used herein, the term “expression control sequence” or “regulatory sequences” are used interchangeably and generally refer to polynucleotide sequences which may affect the expression of coding sequences to which they are operably linked. Expression control sequences may be sequences which control the transcription, post-transcriptional events, and translation of nucleic acid sequences. Expression control sequences may include appropriate transcription initiation, termination, promoter and enhancer sequences; efficient RNA processing signals, such as splicing and poly adenylation signals; sequences that stabilize cytoplasmic mRNA; sequences that enhance translation efficiency (e.g., ribosome binding sites); sequences that enhance protein stability; and when desired, sequences that enhance protein secretion. The nature of such control sequences may differ depending upon the host organism; in prokaryotes, such control sequences generally include promoter, ribosomal binding site, and transcription termination sequence. The term “control sequences” is intended to include, at a minimum, all components whose presence is essential for expression, and can also include additional components whose presence is advantageous, for example, leader sequences and fusion partner sequences.

[0194] In some embodiments, the method for generating an altered cell line comprises contacting an adherent cell line with a recombinant DNA or RNA vector construct carrying a heterologous gene, thereby effecting a modified expression profile of the adherent cell line or derivative thereof. The vector construct may be developed using a specific choice of vector, insertion of the heterologous gene, and choice of promotor, and upon delivery to a cell,genetic manipulation may be acquired wherein gene expression may be up- or down- regulated.

[0195] In some embodiments, a modified expression profile may comprise an up- regulated expression of a heterologous gene. A gene vector may be developed using a specific choice of vector, insertion of the gene, and choice of promotor, and upon insertion into a cell, genetic manipulation may be acquired wherein gene expression may be up- regulated. The vector can be a viral vector (e.g., a retrovirus vector, an adeno-associated virus vector, an adenovirus vector, a herpesvirus vector, or a poxvirus vector) which is employed for the introduction of the DNA or RNA construct into the host cell genome. Non- viral vectors or RNA may be used as well. Random chromosomal integration, or targeted integration (e.g., using a nuclease, transcription activator-like effector nucleases (TALENs), Zinc-finger nucleases (ZFNs), and / or clustered regularly interspaced short palindromic repeats (CRISPRs), or transgene expression (e.g., using a natural or chemically modified RNA) can be used. Other vectors may include cosmids, Yeast artificial chromosomes (YAC), bacterial artificial chromosomes (BACs), shuttle vectors, plasmid vectors, or secretion vectors.

[0196] In some embodiments, the method for generating an altered cell line comprises forced, transient, non-integrative gene expression can be achieved using various nucleic acid molecules such as messenger ribonucleic acid (mRNA), complementary deoxyribonucleic acid (cDNA), micro RNA (miRNA), transfer RNA (tRNA), silencing RNA (siRNA) or any variants, combinations, or analogs thereof. A nucleic acid may be natural in origin or may be a synthetic nucleic acid molecule. Gene expression may be transient, non-integrative such that nucleic acid molecules delivered into a cell are not integrated into the genome of the cell.

[0197] In some embodiments, the method for generating an altered cell may comprise altering, silencing, attenuating, or knocking-out a gene or genetic construct in order to modulate the expression or expression profile an altered cell line. As used herein, the term “knock-out” generally refers to a gene whose level of expression or activity has been reduced to zero. In some instances, a gene can be knocked-out via deletion of some or all of its coding sequence. In other instances, a gene can be knocked-out via introduction of one or more nucleotides into its open reading frame, which results in translation of a non- sense or otherwise non-functional protein product. For example, the altered cells e.g., fish cells), may have the expression mechanism for at least one protein, at least one fat, an oligosaccharide, or at least one amino acid, altered, silenced, attenuated, or knocked-out. Alternatively, or additionally, the gene, genetic construct or expression mechanism for at least one of thefollowing genes can be readily altered, silenced, attenuated, or knocked-out using known methods and reagents, including those described herein.

[0198] In some embodiments, a method for generating an altered cell may comprise mutating a nucleic acid sequence by any method known in the art including but not limited to mutagenesis techniques such as “error-prone PCR” (a process for performing PCR under conditions where the copying fidelity of the DNA polymerase is low, such that a high rate of point mutations is obtained along the entire length of the PCR product; see, e.g., Leung et al., Technique 1:11-15, 1989, and Caldwell and Joyce, PCR Methods Applic. 2:28-33, 1992, each of which is incorporated herein by reference in their entireties for all purposes); and “oligonucleotide-directed mutagenesis” (a process which enables the generation of sitespecific mutations in any cloned DNA segment of interest; see, e.g., Reidhaar-Olson and Sauer, Science 241:53-57, 1988, which is incorporated herein by reference in its entirety for all purposes).

[0199] In some embodiments, the method for generating an altered cell line comprises an altered cell line comprising a gene, a transcript, or a protein selected from the group consisting of ABCG2, SI, NDUFS8, ITGA5, CNTD1, PKHD1L1, PLXNB2, CASP10, FN1, ASAP2, IL13RA2, DAAM2, MCTP1, NUGGC, MEGF10, KIAA1324L, CPXM1, PHACTR4, FGF13, FLT1, PRICKLEI, ZEB1, SULF2, NET1, KIFAP3, HDAC9, DOPEY2, MAN2B2, TLE4, GARNL3, PFKP, ANKS1B, ABHD4, GTPBP2, PLXNA3, CREB3, NLRP12, PTPRK, RGN, GLUL, ABCG2, SI, MMP13, CMYA5, CAMTAI, ABCA1, CDH1, NDUFS8, EPHA10, DCHS1, OLFML1, ITGA5, SLC12A5, F8, CNTD1, PKHD1L1, ARHGAP22, LTBP3, PPP1R42, ADH5, REEP1, ADAMTS1, ATF5, ALDH1L1, ADAMTSL3, PLXNB2, CASP10, CSF1R, BSCL2, SLC15A2, CYP3A4, FN1, KIAA1644, ABCC6, GARS, ANTXRL, ASAP2, GGT7, GARS, P2RY4, ABCA1, IL1B, PRKAG2, TNFAIP3, VASP, FSTL1, IL13RA2, KLHL38, SLC47A2, SLC5A5, FKBP14, MAGI2, GTPBP1, DAAM2, EXOC3L1, RAB37, KRT12, SLCO2B1, ADM2, MCTP1, DACT2, NUGGC, CHRD, ROBO3, MMP19, PTK7, PLEKHH1, MEGF10, FERMT1, SRPX2, TOX3, CTSS, MST1R, CCDC108, SEMA6C, AVPR1A, TSC22D4, FSTL3, ITGA2, PTGIS, COLEC12, KIAA1324L, NLN, FBXO32, CCDC153, CPXM1, PHACTR4, FGF13, DOCKIO, CYSTM1, FAM214A, CAND2, ARHGEF25, PTPLAD2, PAMR1, ULK2, PRODH, KRT8, TRIM55, KIAA1522, OPLAH, PREXI, LRP2, TBC1D2, INVS, FLT1, PRICKLEI, ADAMTS12, MDM2, CSRNP1, RTP4, MED13L, NFKBIA, RGS12, LMNA, RIN1, TCN2, PDE7B, COL23A1, KIAA0141, ANTXRL, AATK, ZEB1, IL1RAP, COL23A1, SULF2, MXRA8, ZMIZ1, TMTC2, KIFAP3, ISG15, MAP6, HDAC9, ACSL3,DOPEY2, MAN2B2, GARNL3, MKL2, ATXN1, WDFY2, CAPN2, ERRFH, FARP1, HFE2, ZC3H12D, PFKP, ANKS1B, UAP1L1, ABHD4, RNF165, MPP5, SAT1, HBP1, AMPD2, HOMEZ, B3GNT2, GTPBP2, STEAP4, PCDHAC2, COL4A3BP, TNS3, RNF169, AEBP1, TFE3, TTYH1, NEIL1, KIAA1033, MMP14, ACSL4, KLHL40, LPIN1, FGD1, XPC, PLXNA3, TNFAIP2, CCDC92, DAB2, MTMR11, ZFYVE28, PC, ADIPOR2, MYODI, ZBTB33, METRNL, TBC1D2B, MFAP5, SCD, PPP1R3C, VPS4B, QPCT, METRNL, CTSH, CREB3, ARHGAP24, WDFY4, ROR2, ATP6V1B2, CTSZ, CXADR, MFSD2A, AVIL, XKRX, NLRP12, PTPRK, CHRNG, TIFA, TMCC3, SEMA4B, GDF10, PARD3, RGN, MAN2B1, PNPLA6, COL15A1, VPS41, TBC1D26, GHDC, ATHL1, NUGGC, TBC1D26, FSTL3, PNPLA6, XKRX, LTBP3, MFAP5, ABCC6, CSF1R, FARP1, SRPX2, LRP2, AATK, KRT12, MCTP1, CCDC153, SLC5A5, KRT8, PAMR1, FN1, HEY1, SCUBE3, MYLPF, MARCKSL1, RAB11FIP1, NTN1, GPT, GPD1, BAIAP2, MFI2, IPO13, ARHGEF28, ATP2A1, S0RBS2, AD API, TLE3, C11ORF54, CD58, MOG, DPYS15, HNRNPL, PDIA3, PLXNB3, HUNK, HEY1, MYLPF, SCUBE3, S0RBS2, ATP2A1, MFI2, BAIAP2, AD API, RAB11FIP1, MARCKSL1, MOG, IPO13, HUNK, ARHGEF28, NTN1, GPD1, GPT, CD58, HNRNPL, PDIA3, DPYS15, TLE3, C11ORF54, PLXNB3, HEY1, IFI27L2, ARHGAP6, SP0N2, SCUBE3, MYLPF, LFNG, HSD3B7, TMEM200B, ABAT, KCTD12, GSTM3, TNNI3, SEMA3E, HES1, UCP2, GALNT15, ADPRHL1, MARCKSL1, RAB11FIP1, ANO8, NTN1, SKAP2, GPT, COX7A2, DKK1, GPD1, BAIAP2, RABEPK, SHD, CEMIP, XYLT1, CPAMD8, PSMB8, FBP1, DLL1, MFI2, TLCD1, IPO13, ANKRD24, GALNT3, ARHGEF28, BCL2L13, THRAP3, SCARA5, MTTP, RANGRF, ATP2A1, WDR83, S0RBS2, ASL, PSMB10, SLC12A8, TM7SF2, AD API, ANXA3, LAMA3, TLE3, FREM2, FAM60A, C11ORF54, MYO16, CD58, ZEB2, STAC3, HYAL2, EMD, CDH2, CRAT, MEI, PLA2G6, LGALS9, DOK7, MOG, HIST1H1E, FRAT2, SLC35D1, BAG2, HNRNPL, C14ORF159, SLC45A3, FMN2, STAC2, TTC28, SLC38A5, PTPRE, LSS, AMOTL2, CACNA1H, GPC5, SLC9A3R1, TPGS1, ARPP21, PLEKHG1, TUBA1A, EIF2AK2, MURC, JPH1, PPP2R3B, BPGM, ARHGAP8, TPCN2, PDIA3, ARSI, IER2, PLXNB3, SPG20, TMEM198B, HUNK, HGD, ALAS1, IFI27L2, ANO8, HEY1V MYLPF, UCP2, ABAT, SCUBE3, ANKRD24, ZEB2, ARHGAP6, S0RBS2, ATP2A1, ADPRHL1, MFI2, HES1, BAIAP2, TNNI3, HIST1H1E, TMEM200B, AD API, SEMA3E, MURC, ALAS1, RAB11FIP1, TTC28, CRAT, MARCKSL1, IER2, MOG, XYLT1, SLC45A3, HSD3B7, IPO13, HYAL2, HUNK, FBP1, ARHGEF28, EMD, AMOTL2, MYO16, GALNT15, GPD1, TGM1, CPAMD8, THRAP3, LAMA3, C14ORF159, FREM2, STAC2, GSTM3, JPH1, SHD, HGD, GPC5, DOK7, STAC3, BCL2L13, KCTD12, BPGM,TUBA1A, GALNT3, GPT, HNRNPL, DKK1, PLEKHG1, ARHGAP8, CEMIP, WDR83, NTN1, MEI, BAG2, CACNA1H, RABEPK, SLC9A3R1, TPCN2, PDIA3, LGALS9, RANGRF, LSS, PPP2R3B, SPG20, TM7SF2, EIF2AK2, PSMB8, SLC38A5, TLCD1, FRAT2, SKAP2, CDH2, ASL, FMN2, ARPP21, TPGS1, FAM60A, PLA2G6, PSMB10, COX7A2, SCARA5, DLL1, TLE3, LFNG, MTTP, TMEM198B, PLXNB3, SPON2, ANXA3, SLC35D1, C11ORF54, PTPRE, and a combination thereof.

[0200] In some embodiments, the method for generating an altered cell line comprises an altered cell line comprising a gene, a transcript, or a protein selected from the group consisting of ABCG2, SI, NDUFS8, ITGA5, CNTD1, PKHD1L1, PLXNB2, CASP10, FN1, ASAP2, IL13RA2, DAAM2, MCTP1, NUGGC, MEGF10, KIAA1324L, CPXM1, PHACTR4, FGF13, FLT1, PRICKLEI, ZEB1, SULF2, NET1, KIFAP3, HDAC9, DOPEY2, MAN2B2, TLE4, GARNL3, PFKP, ANKS1B, ABHD4, GTPBP2, PLXNA3, CREB3, NLRP12, PTPRK, RGN, and a combination thereof.

[0201] In some embodiments, the method for generating an altered cell line comprises an altered cell line comprising a gene, transcript, or protein selected from the group consisting of GLUL, ABCG2, SI, MMP13, CMYA5, CAMTAI, ABCA1, CDH1, NDUFS8, EPHA10, DCHS1, OLFML1, ITGA5, SLC12A5, F8, CNTD1, PKHD1L1, ARHGAP22, LTBP3, PPP1R42, ADH5, REEP1, ADAMTS1, ATF5, ALDH1L1, ADAMTSL3, PLXNB2, CASP10, CSF1R, BSCL2, SLC15A2, CYP3A4, FN1, KIAA1644, ABCC6, GARS, ANTXRL, ASAP2, GGT7, GARS, P2RY4, ABCA1, IL1B, PRKAG2, TNFAIP3, VASP, FSTL1, IL13RA2, KLHL38, SLC47A2, SLC5A5, FKBP14, MAGI2, GTPBP1, DAAM2, EXOC3L1, RAB37, KRT12, SLCO2B1, ADM2, MCTP1, DACT2, NUGGC, CHRD, ROBO3, MMP19, PTK7, PLEKHH1, MEGF10, FERMT1, SRPX2, TOX3, CTSS, MST1R, CCDC108, SEMA6C, AVPR1A, TSC22D4, FSTL3, ITGA2, PTGIS, COLEC12, KIAA1324L, NLN, FBXO32, CCDC153, CPXM1, PHACTR4, FGF13, DOCK10, CYSTM1, FAM214A, CAND2, ARHGEF25, PTPLAD2, PAMR1, ULK2, PRODH, KRT8, TRIM55, KIAA1522, OPLAH, PREXI, LRP2, TBC1D2, INVS, FLT1, PRICKLEI, ADAMTS12, MDM2, CSRNP1, RTP4, MED13L, NFKBIA, RGS12, LMNA, RIN1, TCN2, PDE7B, COL23A1, KIAA0141, ANTXRL, AATK, ZEB1, IL1RAP, COL23A1, SULF2, MXRA8, ZMIZ1, TMTC2, KIFAP3, ISG15, MAP6, HDAC9, ACSL3, DOPEY2, MAN2B2, GARNL3, MKL2, ATXN1, WDFY2, CAPN2, ERRFI1, FARP1, HFE2, ZC3H12D, PFKP, ANKS1B, UAP1L1, ABHD4, RNF165, MPP5, SAT1, HBP1, AMPD2, HOMEZ, B3GNT2, GTPBP2, STEAP4, PCDHAC2, COL4A3BP, TNS3, RNF169, AEBP1, TFE3, TTYH1, NEIL1, KIAA1033, MMP14, ACSL4, KLHL40, LPIN1, FGD1, XPC, PLXNA3, TNFAIP2,CCDC92, DAB2, MTMR11, ZFYVE28, PC, ADIP0R2, MYODI, ZBTB33, METRNL, TBC1D2B, MFAP5, SCD, PPP1R3C, VPS4B, QPCT, METRNL, CTSH, CREB3, ARHGAP24, WDFY4, ROR2, ATP6V1B2, CTSZ, CXADR, MFSD2A, AVIL, XKRX, NLRP12, PTPRK, CHRNG, TIFA, TMCC3, SEMA4B, GDF10, PARD3, RGN, MAN2B1, PNPLA6, COL15A1, VPS41, TBC1D26, GHDC, ATHL1, NUGGC, TBC1D26, FSTL3, PNPLA6, XKRX, LTBP3, MFAP5, ABCC6, CSF1R, FARP1, SRPX2, LRP2, AATK, KRT12, MCTP1, CCDC153, SLC5A5, KRT8, PAMR1, FN1, and a combination thereof.

[0202] In some embodiments, the method for generating an altered cell line comprises an altered cell line comprising a gene, a transcript, or a protein selected from the group consisting of HEY1, SCUBE3, MYLPF, MARCKSL1, RAB11FIP1, NTN1, GPT, GPD1, BAIAP2, MFI2, IPO13, ARHGEF28, ATP2A1, SORBS2, AD API, TLE3, C11ORF54, CD58, MOG, DPYS15, HNRNPL, PDIA3, PLXNB3, HUNK, HEY1, MYLPF, SCUBE3, SORBS2, ATP2A1, MFI2, BAIAP2, AD API, RAB11FIP1, MARCKSL1, MOG, IPO13, HUNK, ARHGEF28, NTN1, GPD1, GPT, CD58, HNRNPL, PDIA3, DPYS15, TLE3, C11ORF54, PLXNB3, and a combination thereof.

[0203] In some embodiments, the method for generating an altered cell line comprises an altered cell line comprising a gene, a transcript, or a protein selected from the group consisting of HEY1, IFI27L2, ARHGAP6, SPON2, SCUBE3, MYLPF, LFNG, HSD3B7, TMEM200B, ABAT, KCTD12, GSTM3, TNNI3, SEMA3E, HES1, UCP2, GALNT15, ADPRHL1, MARCKSL1, RAB11FIP1, ANO8, NTN1, SKAP2, GPT, COX7A2, DKK1, GPD1, BAIAP2, RABEPK, SHD, CEMIP, XYLT1, CPAMD8, PSMB8, FBP1, DLL1, MFI2, TLCD1, IPO13, ANKRD24, GALNT3, ARHGEF28, BCL2L13, THRAP3, SCARA5, MTTP, RANGRF, ATP2A1, WDR83, SORBS2, ASL, PSMB10, SLC12A8, TM7SF2, AD API, ANXA3, LAMA3, TLE3, FREM2, FAM60A, C11ORF54, MY016, CD58, ZEB2, STAC3, HYAL2, EMD, CDH2, CRAT, MEI, PLA2G6, LGALS9, DOK7, MOG, HIST1H1E, FRAT2, SLC35D1, BAG2, HNRNPL, C14ORF159, SLC45A3, FMN2, STAC2, TTC28, SLC38A5, PTPRE, LSS, AMOTL2, CACNA1H, GPC5, SLC9A3R1, TPGS1, ARPP21, PLEKHG1, TUBA1A, EIF2AK2, MURC, JPH1, PPP2R3B, BPGM, ARHGAP8, TPCN2, PDIA3, ARSI, IER2, PLXNB3, SPG20, TMEM198B, HUNK, HGD, ALAS1, IFI27L2, ANO8, HEY1V MYLPF, UCP2, ABAT, SCUBE3, ANKRD24, ZEB2, ARHGAP6, SORBS2, ATP2A1, ADPRHL1, MFI2, HES1, BAIAP2, TNNI3, HIST1H1E, TMEM200B, AD API, SEMA3E, MURC, ALAS1, RAB11FIP1, TTC28, CRAT, MARCKSL1, IER2, MOG, XYLT1, SLC45A3, HSD3B7, IPO13, HYAL2, HUNK, FBP1, ARHGEF28, EMD, AMOTL2, MY016, GALNT15, GPD1, TGM1, CPAMD8, THRAP3, LAMA3,C14ORF159, FREM2, STAC2, GSTM3, JPH1, SHD, HGD, GPC5, D0K7, STAC3, BCL2L13, KCTD12, BPGM, TUBA1A, GALNT3, GPT, HNRNPL, DKK1, PLEKHG1, ARHGAP8, CEMIP, WDR83, NTN1, MEI, BAG2, CACNA1H, RABEPK, SLC9A3R1, TPCN2, PDIA3, LGALS9, RANGRF, LSS, PPP2R3B, SPG20, TM7SF2, EIF2AK2, PSMB8, SLC38A5, TLCD1, FRAT2, SKAP2, CDH2, ASL, FMN2, ARPP21, TPGS1, FAM60A, PLA2G6, PSMB10, COX7A2, SCARA5, DLL1, TLE3, LFNG, MTTP, TMEM198B, PLXNB3, SPON2, ANXA3, SLC35D1, C11ORF54, PTPRE, and a combination thereof.I. Definitions

[0204] As used herein, the singular forms “a,” “an,” and “the” are intended to include the plural forms as well, unless the context clearly indicates otherwise.

[0205] The term “comprising” is intended to mean that the compositions and methods include the recited elements, but do not exclude others.

[0206] “Consisting essentially of’ when used to define compositions and methods, shall mean excluding other elements of any essential significance to the combination. For example, a composition consisting essentially of the elements as defined herein would not exclude other elements that do not materially affect the basic and novel characteristic(s) of the claimed embodiments.

[0207] “Consisting of’ shall mean excluding more than trace amount of other ingredients and substantial method steps recited. Embodiments defined by each of these transition terms are within the scope of this disclosure.

[0208] The term “about” when used before a numerical designation, e.g., temperature, time, amount, concentration, and such other, including a range, indicates approximations which may vary by (+) or (-) 10%, 5%, or 1%. As used herein, and unless otherwise specified, the terms “about” and “approximately,” when used in connection with amounts, contemplate an amount ± 10%, ±5%, ±4%, ±3%, ±2%, ±1%, or ±0.5% of the specified amount. In certain embodiments, “about” can mean ±10%. In certain embodiments, “about” can mean ±5%. In certain embodiments, “about” can mean ±4%. In certain embodiments, “about” can mean ±3%. In certain embodiments, “about” can mean ±2 %. In certain embodiments, “about” can mean ±1%. In certain embodiments, “about” can mean ±0.5%.

[0209] As used herein, the term “adapted Bluefin tuna (BFT) cells” refers to cells that have been adapted to grow in suspension culture (without microcarriers) in medium, without serum.

[0210] As used herein, “cell lines” refers to an important biological tool can be obtained for carrying out research in physiology, virology, pharmacology, toxicology, cancer / carcinogenesis and transgenic fields. Refer to https: / / www.researchgate.net / publication / 270174922_Overview_of_fish_cell_lines_and_their _uses and references cited therein.

[0211] As used herein, “cell culture” is a method used to grow cells in a culture dish or flask within a laboratory environment. The purpose of cell cultures is to enable researchers to study cellular structure, biochemistry, and function. Studies performed using cultured cells are often referred to as in vitro studies (experiments performed in a laboratory vessel, such as a test tube). This contrasts with in vivo studies, which occur within living organisms.

[0212] The term “continuous suspension” means that the cells grow stably in suspension. As a result, a suspension cell line can be obtained.

[0213] The wording “serum- free” specifying the medium for use in the methods of the disclosure refers to the absence of any animal-derived serum, particularly of fetal calf serum, in the medium. The serum-free medium used in the methods of the present disclosure is not particularly limited and may be based on any basal medium such as DMEM, Ham's F12, Medium 199, McCoy or RPMI generally known to the skilled person. The basal medium may comprise several ingredients, including amino acids, vitamins, organic and inorganic salts, and sources of carbohydrate, each ingredient being present in an amount which supports the cultivation of a cell which is generally known to the person skilled in the art. The medium may contain auxiliary substances, such as buffer substances like sodium bicarbonate and / or HEPES, antioxidants, stabilizers to counteract mechanical stress, or protease inhibitors. If required, a non-ionic surfactant such as mixtures of polyethylene glycols and polypropylene glycols (e.g. Pluronic F68 ®, SERVA) can be added as a defoaming agent.

[0214] As used herein, the term “adherent culture” refers to cell culture wherein the cells adhere to a surface, e.g. a tissue culture plate or microcarrier. “Microcarriers” are any carrier, e.g. beads, that provides a surface for cells to adhere other than the surface of the culture vessel.

[0215] As used herein, the term “suspension culture” refers to cell culture in suspension, as opposed to adherent culture, without the use of microcarriers.

[0216] The term “adherent” in the expression “adherent cell line” means that the cells need a surface on which they may grow. The adherent cell line used in the present disclosure may be at least one cell line selected from the group consisting of an analytical cell line, aprimary cell line, or a stem cell line. According to an embodiment of the disclosure, the adherent cell line is a BFT cell line.

[0217] The term “analytical cell line” covers cell lines possessing a metabolic function (e.g. organ-specific enzyme production, steroid secretion), a transgenic reporter gene and / or a specific chemically induced morphological behavior (e.g. phenotypic changes, differentiation). In the present disclosure, the expression “suspension cell line” means that the cells of said cell line can be stably cultured in suspension and in a liquid medium.

[0218] The term “alteration” or “adaptation” of a cell denotes changes made by a cell due to environmental changes, i.e. for example due to a change of the culture medium or a process or technique.

[0219] The term “passage” used herein refers to subculturing cells, wherein some or all cells from a previous culture are transferred to a fresh growth medium. According to a preferred embodiment of the present disclosure, the amount of the serum-substituting supplement in the serum- free medium decreases with the increasing number of passages. By providing the serum- substituting supplement at the beginning of the multitude of number of passages, the initial surviving rate of the cells can be increased by avoiding serum deprivation. At a higher number of passages it is preferred to reduce the amount of the serumsubstituting supplement because of its in later stages obsolete role or the cell line- depending inhibitory effects (e.g. T47D). In a preferred embodiment of the present disclosure, the serum-free medium does not comprise a serum- substituting supplement in the last passage.

[0220] The term “doubling time” refers to the amount of time to increase cell number by two-fold. A lower doubling time indicates a faster growth rate.II. Altered Cell LinesA. Cell Types and Characteristics of Altered Cell Lines

[0221] A variety of cell types may be cultured with the presently disclosed cell culture medium comprising an effective amount of at least two growth factors. In one embodiment, the cells being cultured are derived from a fish species. In another embodiment the cell is derived from preadipocyte lines, myoblast lines and / or fibroblast lines. In one embodiment, the cell is derived from the fish, mahi-mahi. In another embodiment, the cell is derived from the fish, BFT. In another embodiment the cell is derived from the fish, yellowtail.

[0222] In one embodiment, the aquatic species is one or more of Bluefin tuna (Thunnus orientalis, Thunnus maccoyii, and Thunnus ihynnus), yellowfin tuna (Thunnus albacares), yellowtail (e.g., Seriola lalandi), mahi-mahi (Coryphaena hippurus), red snapper (Lutjanuscampechanus), cod (e.g., Gadus morhua, Gadus Macrocephalus, Gadus ogac), flounder, halibut, herring, mackeral, pompano, salmon (Salmo salar), sea bass, Patagonian toothfish (Dissostichus eleginoides), squid, clams, lobster, crabs, scallops, shrimp, eel, bass (e.g., Micropterus scilmoides). bluegill (Lepomis macrochirus), rainbow trout (Oiicorhynchus mykiss), tilapia (Oreochromis massambicus), and carp (e.g., Hypophthalmichthys molilrix).

[0223] In another embodiment, the aquatic species comprises at least one species selected from the group consisting of one of the eight species of tunas in the genus Thunnus. These include the of northern Bluefin tuna (T. thynnus), albacore (T. alalunga), yellowfin tuna (T. albacares), southern Bluefin tuna (T. thynnus maccoyii), bigeye tuna (T. obesus). blackfin tuna (T. allanlicus), Pacific Bluefin tuna (Thunnus orienlalis), and longtail tuna (T. tonggol). See https: / / www.britannica.com / animal / tuna-fish, which is incorporated by reference herein.

[0224] In addition to aquatic species of tuna, cells from a wide variety of fish species can be used. Such species include but are not limited to bass, flounder, hake, scup, smelt, rainbow trout, hardshell clam, blue crab, peekytoe crab, spanner crab, cuttlefish, Eastern oyster, Pacific oyster, anchovy, herring, lingcod, moi, orange roughy, Atlantic Ocean perch, Lake Victoria perch, yellow perch, European oyster, Dover sole, sturgeon, tilefish, wahoo, yellowtail, sea urchin, Atlantic mackerel, sardines, black sea bass, European sea bass, hybrid striped bass, bream, cod, drum, haddock, hoki, Alaska pollock, rockfish, pink salmon, snapper, tilapia, turbot, walleye, lake whitefish, wolffish, hardshell clam, surf clam, cockle, Jonah crab, snow crab, crayfish, bay scallop, Chinese white shrimp, sablefish, Atlantic salmon, coho salmon, skate, dungeness crab, king crab, blue mussel, greenshell mussel, pink shrimp, Escolar, chinook salmon, chum salmon, American shad, Arctic char, carp, catfish, dory, grouper, halibut, monkfish, pompano, abalone, conch, stone crab, American lobster, spiny lobster, octopus, black tiger shrimp, freshwater shrimp, gulf shrimp, Pacific white shrimp, squid, barramundi, cusk, dogfish, kingklip, mahi-mahi, opah, mako shark, swordfish, albacore tuna, yellowfin tuna, geoduck clam, squat lobster, sea scallop, rock shrimp, barracuda, Chilean sea bass, cobia, croaker, eel, blue marlin, mullet, sockeye salmon, Bluefin tuna, shrimp, crabs, lobster, and echinoderms (e.g. sea cucumbers and sea urchins).

[0225] In another embodiment, the cell is one or more of myoblasts, myocytes, preadipocytes, adipocytes, fibroblasts, keratinocytes, epithelial cells, endothelial cells, embryonic derived cells, induced pluripotent stem cells, mesenchymal stem cells, and combinations thereof. In one embodiment, the cell is one or more of myoblasts, preadipocytes, and fibroblasts.

[0226] In another embodiment, the cell line can be selected from the group consisting essentially of preadipocyte lines, myoblast lines and fibroblasts lines. In some embodiments, the aquatic animal cells can be harvested from any desired aquatic animal, in particular, from any fish, mollusk, and / or crustacean, using any suitable method. In another embodiment, the fish for use in the methods of the present disclosure can be one or more of a cartilaginous fish, bony fish, ray-finned fish, lobe-finned fish, mollusks, mussels, cephalopods, crustaceans, and echinoderms.

[0227] In some embodiments, the disclosed suspension cell line exhibits a clumped appearance. In some embodiments, the disclosed suspension cell line exhibits at least one to two cells per aggregate, two to three cells per aggregate, three to four cells per aggregate, four to five cells per aggregate, five to six cells per aggregate, six to seven cells per aggregate, seven to eight cells per aggregate, eight to nine cells per aggregate, or nine to ten cells per aggregate. In a preferred embodiment, the disclosed suspension cell line exhibits five to eight cells per aggregate.

[0228] In some embodiments, the cell aggregate clump size is 100 pm or less in diameter. In some embodiments, the cell aggregate clump size is between 1 to 5 pm in diameter, 5 to 10 pm in diameter, 10 to 15 pm in diameter, 15 to 20 pm in diameter, 20 to 25 pm in diameter, 25 to 30 pm in diameter, 30 to 35 pm in diameter, 35 to 40 pm in diameter, 40 to 50 pm in diameter, 50 to 55 pm in diameter, 55 to 60 pm in diameter, 60 to 65 pm in diameter, 65 to 70 pm in diameter, 70 to 75 pm in diameter, 75 to 80 pm in diameter, 80 to 85 pm in diameter, 85 to 90 pm in diameter, 90 to 100 pm in diameter.

[0229] The disclosed suspension cell line can have increased maximum cell density and reduced doubling time in the medium, shortening the period of suspension adaptation or avoiding the need for suspension adaptation.

[0230] The disclosed suspension cell line can be scaled-up rapidly.

[0231] The disclosed suspension cell lines can be used to produce food for human consumption. The suspension cell lines can also be used to produce food for wild or domesticated animal consumption.B. Cell Culture of Altered Cells

[0232] The disclosed method(s) and cell cultures exhibit improved efficiency and adapt adherent cells to suspension in exponentially less time than currently available methods, reducing the cost and increasing the availability of cell lines for research. The disclosed method(s) and system results in a suspension cell line that can be maintained for at least 4months and / or indefinitely in a suspension culture system), for example, but not limited to a culture system utilizing serum and animal-component free production medium.

[0233] The disclosed method does not require serial serum deprivation steps (e.g., serially transferring the cells to media containing reduced amounts of serum, e.g., 10% then 8% then 4% and etc. until they reach 0%) to passage the cells from serum-containing to serum-free media.

[0234] Additionally, or alternatively, the growth supporting medium may be serum-free medium, medium, or medium lacking animal derived components. Medium are media in which all components have a known chemical structure. Mediums are available from commercial suppliers such as, for example, Sigma and Gibco. Any growth supporting medium that supports cell growth and maintenance under the conditions provided herein may be used. One skilled in the art will be able to suitably select for a particular culture the appropriate medium as well as the other culture variables (see, e.g., Mather J. P. et. Al. (1999) “Culture media, animal cells, large scale production,” Encyclopedia of Bioprocess Technology: Fermentation, Biocatalysis, and Bioseparateion, Vol. 2:777-785 which is hereby incorporated by reference in its entirety).

[0235] Cell dissociation may be achieved by many known methods, for example, but not limited to, adding an effective amount of cell dissociation solution to the cells (e.g., trypsin or EDTA), mechanically dissociating (e.g., cell scraper, pipette, and etc.) or any other mechanical, chemical, enzymatic, or other manner. Cell dissociation may occur without removing the cells from the original culture dish. In one embodiment, this step may involve applying a cell dissociation solution to the surface of the cells (e.g., trypsin or EDTA), immediately pouring off the cell dissociation solution, incubating the treated cells for an appropriate amount of time (e.g., 5 minutes) under appropriate conditions, and resuspending the cells by merely adding new growth supporting media. All of these steps may take place in the original culture dish and without ever removing the cells from the original culture dish.

[0236] A cell dissociation enzyme may comprise a chaotropic agent, or an enzyme, or both. The washing step may optionally be deleted or may be performed on some rounds of the protocol and not on others. The advisability of the washing step is easily determined on a case-by-case basis with the consideration that the washing step may break up the forming cell clumps and may therefore be discontinued or perhaps omitted.

[0237] The disclosed method results in a higher cell density than expression systems employing adherent cells.

[0238] The disclosed method does not rely on microbeads, microcarriers, and other similar devices.

[0239] The growth supporting medium can be a nutrient solution which permits the growth and maintenance of eukaryotic cells and that can provide one or more of the following categories: (1) salts (e.g., sodium, potassium, magnesium, calcium, etc.) contributing to the osmolality of the medium; (2) an energy source, which can be in the form of a carbohydrate such as but not limited to glucose; (3) amino acids, which can be some or all essential amino acids; (4) vitamins and / or other organic compounds; and (5) trace elements, for example, inorganic compounds that may be required at very low concentrations (e.g., micromolar range). The growth supporting solution may optionally be supplemented with one or more components from any of the following categories: (1) animal serum; (2) hormones and other growth factors such as, for example, insulin, transferrin, and epidermal growth factor; and (3) hydrolysates of plant, yeast, and / or tissues, including protein hydrolysates thereof.

[0240] The adapted BFT cell line can be adapted to grow in suspension, in the absence of supporting materials for its adherence (carriers or microcarriers), and in a culture free of serum (e.g., fetal calf serum). This cell line can also be adapted to grow in a suspension as individual cells, in the absence of cell aggregates.C. Cell Culture Process

[0241] Cell culture is a method used to grow cells in a culture dish or flask within a laboratory environment.

[0242] Many kinds of cells can be cultured, including prokaryotic cells such as bacteria, yeasts, and other microorganisms. Cells from higher eukaryotes can also be cultured, although the techniques are more complex than when culturing microorganisms.

[0243] Eukaryotic cell culture typically begins with the primary culture, where cells from higher animals are isolated from original tissue samples. The dissected tissue samples are treated with protein-digesting enzymes to remove extracellular linkages that hold cells together in a tissue form. The dissected tissues are also treated with a chelating agent such as ethylenediamine tetraacetate (EDTA) to remove calcium ions from the tissue, further inhibiting the activity of adhesion molecules between cells. The cells are then gently shaken to help separate them from one another. They can then be selected by type using biochemical techniques such as antibody separation or fluorescence-activated cell sorting (FACS).

[0244] Adherent cell cultures are cultures of cells that grow in a monolayer on a solid substrate such as the bottom of a tissue culture flask. Another term for adherent cells is anchorage-dependent cells since these cells need to adhere or anchor to a solid substrate to proliferate Although no agitation is needed for growth, and trypan blue staining is not needed for passaging, adherent cells do need to be enzymatically or mechanically dissociated from the substrate before passaging.

[0245] Suspension cell cultures are those in which cells float within the culture medium for propagation. These cells do not require a solid substrate and can grow when floating freely in a culture medium. Many cells can be adapted to tolerate suspension cell culture conditions, but some cell types, such as hematopoietic cells, are naturally capable of growing in a suspension cell culture. Agitation is required for growth, but there is no need to dissociate cells prior to passaging.

[0246] Determining when to pass cells to fresh medium in adhesion cell cultures is easier than in a suspension cell culture. Using an inverted microscope, a researcher can visualize cell membrane continuity. By observing the space available on the bottom of the cell culture flask, they can determine how close the culture is to confluence. The cells can be stained with trypan blue or acridine orange and propidium iodine (AO / PI) to identify cell viability and for cell counting purposes.

[0247] There are several advantages to producing seafood from cell cultures rather than whole marine animals. In fact, the production of cell-based seafood has the potential to alter many fundamental parameters attendant whole marine animals such as the production of inedible excess tissues such as bones, skin, shells, and scales, that are often discarded and can negatively impact the environment. Cell-based seafood may also shorten cycle time, as cell cultures of aquatic cells may only require weeks to months to generate functional foods.

[0248] In one aspect, this disclosure relates to a method of culture for generating an adapted cell line that is capable of being cultured in suspension without microcarriers in a medium without serum, said method comprising: a) providing an adherent cell line; b) culturing the adherent cell line in a growth medium comprising 5% (volume / volume, v / v) serum with agitation and in the absence of microcarriers for a period of time sufficient for the cell line to adapt to suspension culture; and c) culturing the suspension-adapted cell line in suspension culture in a medium without serum, thereby providing an adapted cell line that is capable of being cultured in suspension without microcarriers in a medium without serum.

[0249] In one embodiment, step c) includes: culturing the suspension-adapted BFT cell line in suspension culture with an increasing amount of a medium and a decreasing amount of serum (v / v) until the medium represents substantially all of the medium in the culture and substantially all of the serum has been removed, thereby providing an adapted BFT cell line that is capable of being cultured in suspension without microcarriers in a medium without serum.

[0250] In one embodiment, the aquatic species is one or more of Bluefin tuna (Thunnus orientalis, Thunnus maccoyii and Thunnus ihynnus), yellowfin tuna (Thunnus albacares), yellowtail (e.g., Seriola lalandi), mahi-mahi (Coryphaena hippurus), red snapper (Lutjanus campechanus), cod (e.g., Gadus morhua, Gadus Macrocephalus, Gadus ogac), flounder, halibut, herring, mackeral, pompano, salmon (Salmo salar), sea bass, Patagonian toothfish (Dissostichus eleginoides), squid, clams, lobster, crabs, scallops, shrimp, eel, bass (e.g., Micropterus salmoides), bluegill (Lepomis macrochirus), rainbow trout (Oncorhynchus rnykiss), tilapia (Oreochromis massambicus), and carp (e.g., Hypophthalmichthys molitrix).

[0251] In another embodiment, the aquatic species is derived from an aquatic species comprising at least one species selected from the group consisting of one or more of the eight species of tunas in the genus Thunnus. These include the northern Bluefin tuna (T. thynnus), albacore (T. alalunga), yellowfin tuna (T. albacares), southern Bluefin tuna (T. thynnus maccoyii), bigeye tuna (T. obesus), blackfin tuna (T. atlanticus), Pacific Bluefin tuna (Thunnus orientalis), and longtail tuna (T. tonggol).See https: / / www.britannica.com / animal / tuna-fish, which is incorporated by reference herein.

[0252] In another embodiment, the aquatic species is BFT.

[0253] In addition to tuna cells derived from the genus Thunnus, particularly Bluefin tuna cells, cells from a wide variety of fish species can be used. Such species include but are not limited to bass, flounder, hake, scup, smelt, rainbow trout, hardshell clam, blue crab, peekytoe crab, spanner crab, cuttlefish, Eastern oyster, Pacific oyster, anchovy, herring, lingcod, moi, orange roughy, Atlantic Ocean perch, Lake Victoria perch, yellow perch, European oyster, Dover sole, sturgeon, tilefish, wahoo, yellowtail, sea urchin, Atlantic mackerel, sardines, black sea bass, European sea bass, hybrid striped bass, bream, cod, drum, haddock, hoki, Alaska pollock, rockfish, pink salmon, snapper, tilapia, turbot, walleye, lake whitefish, wolffish, hardshell clam, surf clam, cockle, Jonah crab, snow crab, crayfish, bay scallop, Chinese white shrimp, sablefish, Atlantic salmon, coho salmon, skate, dungeness crab, king crab, blue mussel, greenshell mussel, pink shrimp, Escolar, chinook salmon, chum salmon, American shad, Arctic char, carp, catfish, dory, grouper, halibut, monkfish,pompano, abalone, conch, stone crab, American lobster, spiny lobster, octopus, black tiger shrimp, freshwater shrimp, gulf shrimp, Pacific white shrimp, squid, barramundi, cusk, dogfish, kingklip, mahi-mahi, opah, mako shark, swordfish, albacore tuna, yellowfin tuna, geoduck clam, squat lobster, sea scallop, rock shrimp, barracuda, Chilean sea bass, cobia, croaker, eel, blue marlin, mullet, sockeye salmon, Bluefin tuna, shrimp, crabs, lobster, and echinoderms (e.g. sea cucumbers and sea urchins).

[0254] In another embodiment, the cell is one or more of myoblasts, myocytes, preadipocytes, adipocytes, fibroblasts, keratinocytes, epithelial cells, endothelial cells, embryonic derived cells, induced pluripotent stem cells, mesenchymal stem cells, and combinations thereof. In one embodiment, the cell is one or more of myoblasts, preadipocytes, and fibroblasts.

[0255] In another embodiment, the cell line can be preadipocyte lines, myoblast lines and / or fibroblasts lines. In some embodiments, the aquatic animal cells can be harvested from any desired aquatic animal, in particular, from any fish, mollusk, and / or crustacean, using any suitable method. In another embodiment, the fish for use in the methods of the present disclosure can be one or more of a cartilaginous fish, bony fish, ray-finned fish, lobe- finned fish, mollusks, mussels, cephalopods, crustaceans, and echinoderms.

[0256] In one embodiment, the altered cell line can be cultured in an animal component- free growth medium. The altered cell line is capable of growing in suspension culture without microcarriers. In one embodiment, the cells are grown in the presence 0% CO2. In another embodiment, the cells are grown in the presence of at least 1% CO2, at least 1.5% CO2, at least 2% CO2, at least 2.5% CO2, at least 3% CO2, at least 3.5% CO2, at least 4% CO2, at least 4.5% CO2, or at least 5% CO2. In a preferred embodiment, the medium is not exchanged during cell culture stage.

[0257] In one embodiment, the altered cell lines are generally cultured at 20-30° C. at 5% CO2 and 85% relative humidity, more preferably at 27°C. In another embodiment, the cells are generally cultured at 20-30°C and 85% relative humidity, more preferably at 27°C.The altered cell lines can be cultured at about 20° C, 21° C, 22° C, 23° C, 24° C, 25° C, 26° C, 27° C, 28° C, 29° C, or 30° C. In one embodiment, the pH can be from 6.8 to 7.4. In another embodiment the pH may be from 6.5 to 7.8. In another embodiment, the pH may be from 5.6 to 8. The pH can be about 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4., 7.5, 7.6, 7.7, 7.8, 7.9, or 8.0. Other acceptable conditions generally known in the art may also be used.

[0258] In one aspect, cell culture of the altered cell line occurs while scaling up production from a frozen stock to a large bioreactor. In one aspect, the improved mediumallows for at least a four- fold split ratio when passaging the cells (namely lx of cell culture medium containing the cells to be passaged is mixed with 3x of fresh cell culture medium not containing the cells). In another aspect, it allows for a five-fold split ratio, six-fold split ratio, seven-fold split ratio, eight-fold split ratio, nine-fold split ratio, ten-fold split ratio, elevenfold split ratio, twelve-fold split ratio, thirteen-fold split ratio, fourteen-fold split ratio, fifteen-fold split ratio, sixteen-fold split ratio, seventeen-fold split ratio, eighteen-fold split ratio, nineteen-fold split ratio, or twenty-fold split ratio.

[0259] In another aspect, the cells may be continuously cultured in a bioreactor, such as under perfusion conditions for days to months with media exchange of one to four volumes per volume per day.

[0260] In one embodiment, the cells are thawed from a frozen stock. In one embodiment, the cells are in an expansion phase. In another embodiment, the cells are grown in a batch mode, a fed-batch mode, continuous culture, perfusion, or in an integrated bioreactorpurification unit.D. Methods of Altering the Cell Lines

[0261] Cell lines can be altered into suspension cell lines from their adherent parent lines using several different methods of chemical treatments, as known in the art (Chatterjee and Walker, 2017; Lochler et al., 1984; Chen et al., 2023; Brammeld et al., 2017; Chen et al., 2000).

[0262] In one aspect, the disclosure relates to a method for generating an altered cell line, the method comprising (a) providing an adherent cell line or derivative thereof and (b) subjecting said adherent cell line or derivative thereof to a process sufficient to generate an altered expression profile that is different than an expression profile of a corresponding nonaltered cell line. In one embodiment, the altered cell line is a suspension cell line.

[0263] In some embodiments, the cell line can be altered with mutagenesis, chemical mutagens, physical mutagens, electromagnetic radiation, particle radiation, CRISPR, transfection, viruses, or combinations thereof. In some embodiments, the chemical mutagen is an alkylating agent or an azide. In some embodiments, the alkylating agent is N-ethyl-N- nitrosourea (ENU), ethyl methanesulfonate (EMS), or combinations thereof.

[0264] In some embodiments, the method for generating an altered cell line comprises contacting the adherent cell line with a chemical mutagen, a physical mutagen, electromagnetic radiation, particle radiation, a virus, or combinations thereof. In some embodiments, the chemical mutagen is an alkylating agent, azide, or a combination thereof.In some embodiments, the particle radiation is fast neutrons, thermal neutrons, beta particles, alpha particles, or combinations thereof. In some embodiments, the electromagnetic radiation is gamma ray, x-rays, UV light, or combinations thereof.

[0265] In some embodiments, the method for generating an altered cell line comprises contacting the adherent cell line with a heterologous gene including a gene regulating moiety, wherein said gene regulating moiety is configured to regulate an expression of a target gene, a target transcript, or a target protein of the adherent cell line or derivative thereof, thereby effecting a modified expression profile of the target gene, the transcript, or the target protein in the altered suspension cell line as compared to the corresponding non-altered cell line. In some embodiments, the gene regulating moiety is an endonuclease. In some embodiments, the endonuclease is a clustered regularly interspaced short palindromic repeats (CRISPR)- associated (CAS) endonuclease.

[0266] In some embodiments, the method for generating an altered cell line comprises contacting an adherent cell line with a recombinant DNA or RNA vector construct carrying a heterologous gene, thereby effecting a modified expression profile of the adherent cell line or derivative thereof. The vector construct may be developed using a specific choice of vector, insertion of the heterologous gene, and choice of promoter, and upon delivery to a cell, genetic manipulation may be acquired wherein gene expression may be up- or down- regulated. The vector can be a viral vector (e.g., a retrovirus vector, an adeno-associated virus vector, an adenovirus vector, a herpesvirus vector, or a poxvirus vector) which is employed for the introduction of the DNA or RNA construct into the host cell genome. Non- viral vectors or RNA may be used as well. Random chromosomal integration, or targeted integration (e.g., using a nuclease, transcription activator-like effector nucleases (TALENs), Zinc-finger nucleases (ZFNs), and / or clustered regularly interspaced short palindromic repeats (CRISPRs), or transgene expression (e.g., using a natural or chemically modified RNA) can be used. Other vectors may include cosmids, Yeast artificial chromosomes (YAC), bacterial artificial chromosomes (BACs), shuttle vectors, plasmid vectors, or secretion vectors.

[0267] In some embodiments, the method for generating an altered cell line comprises forced, transient, non-integrative gene expression can be achieved using various nucleic acid molecules such as messenger ribonucleic acid (mRNA), complementary deoxyribonucleic acid (cDNA), micro RNA (miRNA), transfer RNA (tRNA), silencing RNA (siRNA) or any variants, combinations, or analogs thereof. A nucleic acid may be natural in origin or may bea synthetic nucleic acid molecule. Gene expression may be transient, non-integrative such that nucleic acid molecules delivered into a cell are not integrated into the genome of the cell.

[0268] In some embodiments, the method for generating an altered cell may comprise altering, silencing, attenuating, or knocking-out a gene or genetic construct in order to modulate the expression or expression profile an altered cell line. As used herein, the term “knock-out” generally refers to a gene whose level of expression or activity has been reduced to zero. In some instances, a gene can be knocked-out via deletion of some or all of its coding sequence. In other instances, a gene can be knocked-out via introduction of one or more nucleotides into its open reading frame, which results in translation of a non- sense or otherwise non-functional protein product. For example, the altered cells (e.g., fish cells), may have the expression mechanism for at least one protein, at least one fat, an oligosaccharide, or at least one amino acid, altered, silenced, attenuated, or knocked-out. Alternatively, or additionally, the gene, genetic construct or expression mechanism for at least one of the following genes can be readily altered, silenced, attenuated, or knocked-out using known methods and reagents, including those described herein.

[0269] In some embodiments, a method for generating an altered cell may comprise mutating a nucleic acid sequence by any method known in the art including but not limited to mutagenesis techniques such as “error-prone PCR” (a process for performing PCR under conditions where the copying fidelity of the DNA polymerase is low, such that a high rate of point mutations is obtained along the entire length of the PCR product; see, e.g., Leung et al., Technique 1:11-15, 1989, and Caldwell and Joyce, PCR Methods Applic. 2:28-33, 1992, each of which is incorporated herein by reference in their entireties for all purposes); and “oligonucleotide-directed mutagenesis” (a process which enables the generation of sitespecific mutations in any cloned DNA segment of interest; see, e.g., Reidhaar-Olson and Sauer, Science 241:53-57, 1988, which is incorporated herein by reference in its entirety for all purposes).III. Exemplary Embodiments

[0270] Among the provided embodiments are:1. A composition, comprising an altered cell line that has an altered expression profile as compared to an expression profile of a corresponding non-altered cell line, wherein the altered cell line is a suspension cell line.2. A composition, comprising an altered cell line that has an altered expression profile as compared to an expression profile of a reference non-altered cell line, wherein the altered cell like is a suspension cell line.3. The composition of embodiment 1 or 2, wherein the altered expression profile comprises an altered gene expression profile and / or an altered phenotypic profile.4. The composition of embodiment 3, wherein the altered phenotypic profile comprises of improved viability and stable growth rates in (1) non-adherent, suspension cell culture, (2) serum-free media cell culture, and / or (3) animal component-free media cell culture.5. The composition of any one of embodiments 1-4, wherein the altered expression profile comprises an upregulated gene expression profile.6. The composition of any one of embodiments 1-4, wherein the altered expression profile comprises a downregulated gene expression profile.7. The composition of any one of embodiments 1-6, wherein the altered expression profile comprises a change to a gene, a transcript, or a protein selected from the group consisting of ABCG2, SI, NDUFS8, ITGA5, CNTD1, PKHD1L1, PLXNB2, CASP10, FN1, ASAP2, IL13RA2, DAAM2, MCTP1, NUGGC, MEGF10, KIAA1324L, CPXM1, PHACTR4, FGF13, FLT1, PRICKLEI, ZEB1, SULF2, NET1, KIFAP3, HDAC9, D0PEY2, MAN2B2, TLE4, GARNL3, PFKP, ANKS1B, ABHD4, GTPBP2, PLXNA3, CREB3, NLRP12, PTPRK, RGN, GLUL, MMP13, CMYA5, CAMTAI, ABCA1, CDH1, EPHA10, DCHS1, 0LFML1, SLC12A5, F8, ARHGAP22, LTBP3, PPP1R42, ADH5, REEP1, ADAMTS1, ATF5, ALDH1L1, ADAMTSL3, CSF1R, BSCL2, SLC15A2, CYP3A4, KIAA1644, ABCC6, GARS, ANTXRL, GGT7, P2RY4, IL1B, PRKAG2, TNFAIP3, VASP, FSTL1, KLHL38, SLC47A2, SLC5A5, FKBP14, MAGI2, GTPBP1, EX0C3L1, RAB37, KRT12, SLCO2B1, ADM2, DACT2, CHRD, R0B03, MMP19, PTK7, PLEKHH1, FERMT1, SRPX2, T0X3, CTSS, MST1R, CCDC108, SEMA6C, AVPR1A, TSC22D4, FSTL3, ITGA2, PTGIS, COLEC12, NLN, FBXO32, CCDC153, DOCKIO, CYSTM1, FAM214A, CAND2, ARHGEF25, PTPLAD2, PAMR1, ULK2, PRODH, KRT8, TRIM55, KIAA1522, OPLAH, PREXI, LRP2, TBC1D2, INVS, ADAMTS12, MDM2, CSRNP1, RTP4, MED13L, NFKBIA, RGS12, LMNA, RIN1, TCN2, PDE7B, COL23A1, KIAA0141, AATK, IL1RAP, MXRA8, ZMIZ1, TMTC2, ISG15, MAP6, ACSL3, MKL2, ATXN1, WDFY2, CAPN2, ERRFI1, FARP1, HFE2, ZC3H12D, UAP1L1, RNF165, MPP5, SAT1, HBP1, AMPD2, HOMEZ, B3GNT2, STEAP4, PCDHAC2, COL4A3BP, TNS3, RNF169, AEBP1, TFE3, TTYH1, NEIL1, KIAA1033, MMP14, ACSL4, KLHL40, LPIN1, FGD1, XPC,TNFAIP2, CCDC92, DAB2, MTMR11, ZFYVE28, PC, ADIP0R2, MYODI, ZBTB33, METRNL, TBC1D2B,MFAP5, SCD, PPP1R3C, VPS4B, QPCT, CTSH, ARHGAP24, WDFY4, R0R2, ATP6V1B2, CTSZ, CXADR, MFSD2A, AVIL, XKRX, CHRNG, TIFA, TMCC3, SEMA4B, GDF10, PARD3, MAN2B1, PNPLA6, COL15A1, VPS41, TBC1D26, GHDC, HEY1, SCUBE3, MYLPF, MARCKSL1, RAB11FIP1, NTN1, GPT, GPD1, BAIAP2, MFI2, IPO13, ARHGEF28, ATP2A1, SORBS2, AD API, TLE3, C11ORF54, CD58, MOG, DPYS15, HNRNPL, PDIA3, PLXNB3, HUNK, HEY1, IFI27L2, ARHGAP6, SPON2, LFNG, HSD3B7, TMEM200B, ABAT, KCTD12, GSTM3, TNNI3, SEMA3E, HES1, UCP2, GALNT15, ADPRHL1, ANO8, SKAP2, COX7A2, DKK1, RABEPK, SHD, CEMIP, XYLT1, CPAMD8, PSMB8, FBP1, DLL1, TLCD1, ANKRD24, GALNT3, BCL2L13, THRAP3, SCARA5, MTTP, RANGRF, WDR83, ASL, PSMB10, SLC12A8, TM7SF2, ANXA3, LAMA3, FREM2, FAM60A, MYO16, ZEB2, STAC3, HYAL2, EMD, CDH2, CRAT, MEI, PLA2G6, LGALS9, DOK7, HIST1H1E, FRAT2, SLC35D1, BAG2, C14ORF159, SLC45A3, FMN2, STAC2, TTC28, SLC38A5, PTPRE, LSS, AMOTL2, CACNA1H, GPC5, SLC9A3R1, TPGS1, ARPP21, PLEKHG1, TUBA1A, EIF2AK2, MURC, JPH1, PPP2R3B, BPGM, ARHGAP8, TPCN2, ARSI, IER2, SPG20, TMEM198B, HGD, ALAS1, TGM1, and a combination thereof.8. The composition of embodiments any one of embodiments 1-5 or 7, wherein the altered expression profile comprises a change to a gene, a transcript, or a protein selected from the group consisting of ABCG2, SI, NDUFS8, ITGA5, CNTD1, PKHD1L1, PLXNB2, CASP10, FN1, ASAP2, IL13RA2, DAAM2, MCTP1, NUGGC, MEGF10, KIAA1324L, CPXM1, PHACTR4, FGF13, FLT1, PRICKLEI, ZEB1, SULF2, NET1, KIFAP3, HDAC9, DOPEY2, MAN2B2, TLE4, GARNL3, PFKP, ANKS1B, ABHD4, GTPBP2, PLXNA3, CREB3, NLRP12, PTPRK, RGN, GLUL, and a combination thereof.9. The composition of embodiment 8, wherein the change to the selected gene, transcript, or protein comprises a genetic variant comprising a deleterious effect on the resulting protein, compared to an effect of a non-variant gene of a corresponding or reference non-altered cell line or a reference genome.10. The composition of embodiment 8 or 9, wherein the change to the selected gene, transcript, or protein comprises a genetic variant comprising a frameshift, a nonsense, a stop codon, or a loss of function mutation.11. The composition of embodiment 9 or 10, wherein the deleterious effect comprises protein truncation, loss of protein function, and / or triggering of nonsense-mediated protein decay.12. The composition of any one of embodiments 8-11, wherein the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein theselected gene is upregulated by a change of about 0.5 to about 14 log fold, about 0.5 to about 12 log fold, 0.5 to about 10 log fold, about 0.5 to about 8 log fold, about 0.5 to about 6 log fold, about 0.5 to about 4 log fold, or about 0.5 to about 2 log fold, each inclusive, compared to a reference expression level of the selected gene.13. The composition of any one of embodiments 8-12, wherein the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is upregulated by a change of about 1.0 log fold, about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, 7.0 log fold, about 7.5 log fold, about 8.0 log fold, about 8.5 log fold, about 9.0 log fold, about 9.5 log fold, or about 10.0 log fold, compared to a reference expression level of the selected gene.14. The composition of any one of embodiments 1-5 or 7, wherein the altered expression profile comprises a change to a gene, a transcript, or a protein selected from the group consisting of GLUL, ABCG2, SI, MMP13, CMYA5, CAMTAI, ABCA1, CDH1, NDUFS8, EPHA10, DCHS1, OLFML1, ITGA5, SLC12A5, F8, CNTD1, PKHD1L1, ARHGAP22, LTBP3, PPP1R42, ADH5, REEP1, ADAMTS1, ATF5, ALDH1L1, ADAMTSL3, PLXNB2, CASP10, CSF1R, BSCL2, SLC15A2, CYP3A4, FN1, KIAA1644, ABCC6, GARS, ANTXRL, ASAP2, GGT7, GARS, P2RY4, ABCA1, IL1B, PRKAG2, TNFAIP3, VASP, FSTL1, IL13RA2, KLHL38, SLC47A2, SLC5A5, FKBP14, MAGI2, GTPBP1, DAAM2, EXOC3L1, RAB37, KRT12, SLCO2B1, ADM2, MCTP1, DACT2, NUGGC, CHRD, ROBO3, MMP19, PTK7, PLEKHH1, MEGF10, FERMT1, SRPX2, TOX3, CTSS, MST1R, CCDC108, SEMA6C, AVPR1A, TSC22D4, FSTL3, ITGA2, PTGIS, COLEC12, KIAA1324L, NLN, FBXO32, CCDC153, CPXM1, PHACTR4, FGF13, DOCK10, CYSTM1, FAM214A, CAND2, ARHGEF25, PTPLAD2, PAMR1, ULK2, PRODH, KRT8, TRIM55, KIAA1522, OPLAH, PREXI, LRP2, TBC1D2, INVS, FLT1, PRICKLEI, ADAMTS12, MDM2, CSRNP1, RTP4, MED13L, NFKBIA, RGS12, LMNA, RIN1, TCN2, PDE7B, COL23A1, KIAA0141, ANTXRL, AATK, ZEB1, IL1RAP, COL23A1, SULF2, MXRA8, ZMIZ1, TMTC2, KIFAP3, ISG15, MAP6, HDAC9, ACSL3, DOPEY2, MAN2B2, GARNL3, MKL2, ATXN1, WDFY2, CAPN2, ERRFI1, FARP1, HFE2, ZC3H12D, PFKP, ANKS1B, UAP1L1, ABHD4, RNF165, MPP5, SAT1, HBP1, AMPD2, HOMEZ, B3GNT2, GTPBP2, STEAP4, PCDHAC2, COL4A3BP, TNS3, RNF169, AEBP1, TFE3, TTYH1, NEIL1, KIAA1033, MMP14, ACSL4, KLHL40, LPIN1, FGD1, XPC, PLXNA3, TNFAIP2, CCDC92, DAB2, MTMR11, ZFYVE28, PC, ADIPOR2, MYODI, ZBTB33, METRNL, TBC1D2B, MFAP5, SCD, PPP1R3C, VPS4B, QPCT, METRNL, CTSH, CREB3,ARHGAP24, WDFY4, R0R2, ATP6V1B2, CTSZ, CXADR, MFSD2A, AVIL, XKRX, NLRP12, PTPRK, CHRNG, TIFA, TMCC3, SEMA4B, GDF10, PARD3, RGN, MAN2B1, PNPLA6, COL15A1, VPS41, TBC1D26, GHDC, ATHL1, and a combination thereof.15. The composition of embodiment 14, wherein the change to the selected gene, transcript, or protein comprises a genetic variant comprising a non-deleterious effect on the resulting protein, compared an effect of a non-variant gene of a corresponding or reference non-altered cell line or a reference genome.16. The composition of embodiment 14 or 15, wherein the change to the selected gene, transcript, or protein comprises a genetic variant comprising an intragenic or an intron variant.17. The composition of embodiment 15 or 16, wherein the non-deleterious effect comprises an alteration or a change in effectiveness of the resulting protein.18. The composition of embodiment 17, wherein the effectiveness of the resulting protein is decreased.19. The composition of embodiment 17, wherein the effectiveness of the resulting protein is increased.20. The composition of any one of embodiments 14-19, wherein the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is upregulated by a change of about 0.5 to about 14 log fold, about 0.5 to about 12 log fold, 0.5 to about 10 log fold, about 0.5 to about 8 log fold, about 0.5 to about 6 log fold, about 0.5 to about 4 log fold, or about 0.5 to about 2 log fold, each inclusive, compared to a reference expression level of the selected gene.21. The composition of any one of embodiments 14-20, wherein the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is upregulated by a change of about 1.0 log fold, about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, 7.0 log fold, about 7.5 log fold, about 8.0 log fold, about 8.5 log fold, about 9.0 log fold, about 9.5 log fold, or about 10.0 log fold, compared to a reference expression level of the selected gene.22. The composition of any one of embodiments 1-4 or 6-7, wherein the altered expression profile comprises a change to a gene, a transcript, or a protein selected from the group consisting of HEY1, SCUBE3, MYLPF, MARCKSL1, RAB11FIP1, NTN1, GPT, GPD1, BAIAP2, MFI2, IPO13, ARHGEF28, ATP2A1, SORBS2, AD API, TLE3, Cl 1ORF54, CD58, MOG, DPYS15, HNRNPL, PDIA3, PLXNB3, HUNK, and a combination thereof.23. The composition of embodiment 22, wherein the selected gene, transcript, or protein comprises a genetic variant comprising a deleterious effect on the resulting protein, compared to a non-variant gene of a corresponding or reference non-altered cell line or a reference genome.24. The composition of embodiment 22 or 23, wherein the change to the selected gene, transcript, or protein comprises a genetic variant comprising a frameshift, a nonsense, a stop codon, or a loss of function mutation.25. The composition of embodiment 23 or 24, wherein the deleterious effect comprises protein truncation, loss of protein function, and / or triggering of nonsense-mediated protein decay.26. The composition of any one of embodiments 22-25, wherein the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is downregulated by a change of about 0.5 to about 14 log fold, about 0.5 to about 12 log fold, 0.5 to about 10 log fold, about 0.5 to about 8 log fold, about 0.5 to about 6 log fold, about 0.5 to about 4 log fold, or about 0.5 to about 2 log fold, each inclusive, compared to a reference expression level of the selected gene.27. The composition of any one of embodiments 22-26, wherein the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is downregulated by a change of about 1.0 log fold, about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, 7.0 log fold, about 7.5 log fold, about 8.0 log fold, about 8.5 log fold, about 9.0 log fold, about 9.5 log fold, or about 10.0 log fold, compared to a reference expression level of the selected gene.28. The composition of any one of embodiments 1-4 or 6-7, wherein the altered expression profile comprises a change to a gene, a transcript, or a protein selected from the group consisting of HEY1, IFI27L2, ARHGAP6, SPON2, SCUBE3, MYLPF, LFNG, HSD3B7, TMEM200B, ABAT, KCTD12, GSTM3, TNNI3, SEMA3E, HES1, UCP2, GALNT15, ADPRHL1, MARCKSL1, RAB11FIP1, ANO8, NTN1, SKAP2, GPT, COX7A2, DKK1, GPD1, BAIAP2, RABEPK, SHD, CEMIP, XYLT1, CPAMD8, PSMB8, FBP1, DLL1, MFI2, TLCD1, IPO13, ANKRD24, GALNT3, ARHGEF28, BCL2L13, THRAP3, SCARA5, MTTP, RANGRF, ATP2A1, WDR83, SORBS2, ASL, PSMB10, SLC12A8, TM7SF2, AD API, ANXA3, LAMA3, TLE3, FREM2, FAM60A, C11ORF54, MY016, CD58, ZEB2, STAC3, HYAL2, EMD, CDH2, CRAT, MEI, PLA2G6, LGALS9, D0K7, MOG, HIST1H1E, FRAT2, SLC35D1, BAG2, HNRNPL, C14ORF159, SLC45A3, FMN2, STAC2, TTC28,SLC38A5, PTPRE, LSS, AMOTL2, CACNA1H, GPC5, SLC9A3R1, TPGS1, ARPP21, PLEKHG1, TUBA1A, EIF2AK2, MURC, JPH1, PPP2R3B, BPGM, ARHGAP8, TPCN2, PDIA3, ARSI, IER2, PLXNB3, SPG20, TMEM198B, HUNK, HGD, ALAS1, TGM1, and a combination thereof.29. The composition of embodiment 28, wherein the change to the selected gene, transcript, or protein comprises a genetic variant comprising a non-deleterious effect on the resulting protein, compared an effect of a non-variant gene of a corresponding or reference non-altered cell line or a reference genome.30. The composition of embodiment 28 or 29, wherein the change to the selected gene, transcript, or protein comprises a genetic variant comprising an intragenic or an intron variant.31. The composition of embodiment 29 or 30, wherein the non-deleterious effect comprises an alteration or a change in effectiveness of the resulting protein.32. The composition of embodiment 31, wherein the effectiveness of the resulting protein is decreased.33. The composition of embodiment 31, wherein the effectiveness of the resulting protein is increased.34. The composition of any one of embodiments 28-33, wherein the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is downregulated by a change of about 0.5 to about 14 log fold, about 0.5 to about 12 log fold, 0.5 to about 10 log fold, about 0.5 to about 8 log fold, about 0.5 to about 6 log fold, about 0.5 to about 4 log fold, or about 0.5 to about 2 log fold, each inclusive, compared to a reference expression level of the selected gene.35. The composition of any one of embodiments 28-34, wherein the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is downregulated by a change of about 1.0 log fold, about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, 7.0 log fold, about 7.5 log fold, about 8.0 log fold, about 8.5 log fold, about 9.0 log fold, about 9.5 log fold, or about 10.0 log fold, compared to a reference expression level of the selected gene.36. The composition of any one of embodiments 1-35, wherein the altered cell line has been altered with mutagenesis, chemical mutagens, physical mutagens, electromagnetic radiation, particle radiation, CRISPR, transfection, viruses, non-integrative nucleic acid molecules, or a combination thereof.37. The composition of any one of embodiments 1-36, wherein the altered cell line has been altered with alkylating agents and azides.38. The composition of any one of embodiments 1-37, wherein the altered cell line has been altered with alkylating agents selected from the group consisting of N-ethyl-N-nitrosourea (ENU), ethyl methanesulfonate (EMS), and a combination thereof.39. The composition of any one of embodiments 1-36, wherein the altered cell line has been altered with electromagnetic radiation selected from the group consisting of gamma rays, x-rays, UV light, and a combination thereof.40. The composition of any one of embodiments 1-36, wherein the altered cell line has been altered with particle radiation selected from the group consisting of fast neutrons, thermal neutrons, beta particles, alpha particles, and a combination thereof.41. The composition of any one of embodiments 1-40, wherein the altered cell line, the non-altered cell line, and / or the reference genome is derived from an aquatic species comprising at least one species selected from the group consisting of Bluefin tuna (Thunnus orientalis, Thunnus maccoyii, and Thunnus thynnus), yellowfin tuna (Thunnus albacares), yellowtail (e.g., Seriola lalandi), mahi-mahi (Coryphaena hippurus). red snapper (Lutjanus campechanus). cod (e.g., Gadus morhua, Gadus Macrocephalus, Gadus ogac), flounder, halibut, herring, mackeral, pompano, salmon (Salmo salar), sea bass, Patagonian toothfish (Dissostichus eleginoides), squid, clams, lobster, crabs, scallops, shrimp, eel, bass (e.g., Micropterus salmoides), bluegill (Lepomis macrochirus), rainbow trout (Oncorhynchus rnykiss), tilapia (Oreochromis massambicus), and carp (e.g., Hypophthalmichthys molitrix).42. The composition of any one of embodiments 1-41, wherein the altered cell line, the non-altered cell line, and / or the reference genome is derived from an aquatic species comprising at least one species selected from the group consisting of northern Bluefin tuna (T. thynnus), albacore (T. alalunga), yellowfin tuna (T. albacares), southern Bluefin tuna (T. thynnus maccoyii), bigeye tuna (T. obesus), blackfin tuna (T. atlanticus), Pacific Bluefin tuna (Thunnus orientalis), and longtail tuna (T. tonggol).43. The composition of any one of embodiments 1-40, wherein the altered cell line, the non-altered cell line, and / or the reference genome is derived an aquatic species comprising at least one species selected from the group consisting of bass, flounder, hake, scup, smelt, rainbow trout, hardshell clam, blue crab, peekytoe crab, spanner crab, cuttlefish, Eastern oyster, Pacific oyster, anchovy, herring, lingcod, moi, orange roughy, Atlantic Ocean perch, Lake Victoria perch, yellow perch, European oyster, Dover sole, sturgeon, tilefish, wahoo, yellowtail, sea urchin, Atlantic mackerel, sardines, black sea bass, European sea bass, hybridstriped bass, bream, cod, drum, haddock, hoki, Alaska pollock, rockfish, pink salmon, snapper, tilapia, turbot, walleye, lake whitefish, wolffish, hardshell clam, surf clam, cockle, Jonah crab, snow crab, crayfish, bay scallop, Chinese white shrimp, sablefish, Atlantic salmon, coho salmon, skate, dungeness crab, king crab, blue mussel, greenshell mussel, pink shrimp, Escolar, chinook salmon, chum salmon, American shad, Arctic char, carp, catfish, dory, grouper, halibut, monkfish, pompano, abalone, conch, stone crab, American lobster, spiny lobster, octopus, black tiger shrimp, freshwater shrimp, gulf shrimp, Pacific white shrimp, squid, barramundi, cusk, dogfish, kingklip, mahi-mahi, opah, mako shark, swordfish, albacore tuna, yellowfin tuna, geoduck clam, squat lobster, sea scallop, rock shrimp, barracuda, Chilean sea bass, cobia, croaker, eel, blue marlin, mullet, sockeye salmon, Bluefin tuna, shrimp, crabs, lobster, and echinoderms (e.g. sea cucumbers and sea urchins).44. The composition of any one of embodiments 1-43, wherein the altered cell line, the non-altered cell line, and / or the reference genome is derived from Bluefin tuna (Thunnus orientalis, Thunnus maccoyii, and Thunnus ihynnus).45. A method for generating an altered cell line, the method comprising(a) providing an adherent cell line or derivative thereof; and(b) subjecting the adherent cell line or derivative thereof to a process sufficient to generate an altered cell line comprising an altered expression profile that is different than an expression profile of a corresponding non-altered cell line.46. A method for generating an altered cell line, the method comprising(a) providing an adherent cell line or derivative thereof; and(b) subjecting the adherent cell line or derivative thereof to a process sufficient to generate an altered cell line comprising an altered expression profile comprising:(1) an altered gene expression profile that is different than a gene expression profile of the adherent cell line or derivative used in (a) and / or a reference non-altered cell line; and / or(2) an altered phenotypic profile that is different than a phenotypic profile of the adherent cell line or derivative used in (a) and / or a reference non-altered cell line.47. The composition of embodiment 46, wherein the altered phenotypic profile comprises of improved viability and stabilized growth rates in (1) non-adherent, suspension cell culture, (2) serum-free media cell culture, and / or (3) animal component-free media culture.48. The method of any one of embodiments 45-47, wherein the altered cell line is a suspension cell line.49. The method of any one of embodiments 45-47, wherein the altered cell line is an altered adherent cell line.50. The method of any one of embodiments 45-49, wherein the subjecting in step (b) is performed in vitro.51. The method of any one of embodiments 45-50, wherein the adherent cell line or derivative, the generated altered cell line, and / or the non-altered cell line is derived from an aquatic species.52. The method of any one of embodiments 45-51, wherein the adherent cell line or derivative, the generated altered cell line, and / or the non-altered cell line is derived from an aquatic species comprising at least one species selected from the group consisting of Bluefin tuna (Thunnus orientalis and Thunnus thynnus), yellowfin tuna (Thunnus albacares), yellowtail (e.g., Seriola lalandi), mahi-mahi (Coryphaena hippurus). red snapper (Lutjanus campechanus), cod (e.g., Gadus morhua, Gadus Macrocephalus, Gadus ogac), flounder, halibut, herring, mackeral, pompano, salmon (Salmo salar), sea bass, Patagonian toothfish (Dissostichus eleginoides), squid, clams, lobster, crabs, scallops, shrimp, eel, bass (e.g., Micropterus salmoides), bluegill (Lepomis macrochirus), rainbow trout (Oncorhynchus rnykiss), tilapia (Oreochromis massambicus), and carp (e.g., Hypophthalmichthys molitrix).53. The method of any one of embodiments 45-52, wherein the adherent cell line or derivative, the generated altered cell line, and / or the non-altered cell line is derived from an aquatic species comprising at least one species selected from the group consisting of northern Bluefin tuna (T. thynnus), albacore (T. alalunga), yellowfin tuna (T. albacares), southern Bluefin tuna (T. thynnus maccoyii), bigeye tuna (T. obesus), blackfin tuna (T. atlanticus), Pacific Bluefin tuna (Thunnus orientalis), and longtail tuna (T. tonggol).54. The method of any one of embodiments 45-51, wherein the adherent cell line or derivative, the generated altered cell line, and / or the non-altered cell line is derived from an aquatic species comprising at least one species selected from the group consisting of bass, flounder, hake, scup, smelt, rainbow trout, hardshell clam, blue crab, peekytoe crab, spanner crab, cuttlefish, Eastern oyster, Pacific oyster, anchovy, herring, lingcod, moi, orange roughy, Atlantic Ocean perch, Lake Victoria perch, yellow perch, European oyster, Dover sole, sturgeon, tilefish, wahoo, yellowtail, sea urchin, Atlantic mackerel, sardines, black sea bass, European sea bass, hybrid striped bass, bream, cod, drum, haddock, hoki, Alaska pollock, rockfish, pink salmon, snapper, tilapia, turbot, walleye, lake whitefish, wolffish, hardshell clam, surf clam, cockle, Jonah crab, snow crab, crayfish, bay scallop, Chinese white shrimp, sablefish, Atlantic salmon, coho salmon, skate, dungeness crab, king crab, blue mussel,greenshell mussel, pink shrimp, Escolar, chinook salmon, chum salmon, American shad, Arctic char, carp, catfish, dory, grouper, halibut, monkfish, pompano, abalone, conch, stone crab, American lobster, spiny lobster, octopus, black tiger shrimp, freshwater shrimp, gulf shrimp, Pacific white shrimp, squid, barramundi, cusk, dogfish, kingklip, mahi-mahi, opah, mako shark, swordfish, albacore tuna, yellowfin tuna, geoduck clam, squat lobster, sea scallop, rock shrimp, barracuda, Chilean sea bass, cobia, croaker, eel, blue marlin, mullet, sockeye salmon, Bluefin tuna, shrimp, crabs, lobster, and echinoderms (e.g. sea cucumbers and sea urchins).55. The method of any one of embodiments 45-54, wherein the process sufficient to generate the altered cell line comprises contacting the adherent cell line or derivative thereof with a chemical mutagen, a physical mutagen, electromagnetic radiation, particle radiation, a virus, non-integrative nucleic acid molecules, or a combination thereof.56. The method of any one of embodiments 45-54, wherein the process sufficient to generate the altered cell line comprises contacting the adherent cell line or derivative thereof with an heterologous gene including a gene regulating moiety, wherein the gene regulating moiety is configured to regulate and / or modify an expression of a target gene, a target transcript, or a target protein of the adherent cell line or derivative thereof, thereby effecting the altered expression profile of the target gene, the transcript, or the target protein in the altered cell line as compared to the corresponding or reference non-altered cell line.57. The method of any one of embodiments 45-56, wherein the altered expression profile comprises an upregulated gene expression profile.58. The method of any one of embodiments 45-56, wherein the altered expression profile comprises a downregulated gene expression profile.59. The method of any one of embodiments 45-58, wherein the altered cell line and / or the altered expression profile comprises a change to a gene, a transcript, or a protein selected from the group consisting of ABCG2, SI, NDUFS8, ITGA5, CNTD1, PKHD1L1, PLXNB2, CASP10, FN1, ASAP2, IL13RA2, DAAM2, MCTP1, NUGGC, MEGF10, KIAA1324L, CPXM1, PHACTR4, FGF13, FLT1, PRICKLEI, ZEB1, SULF2, NET1, KIFAP3, HDAC9, DOPEY2, MAN2B2, TLE4, GARNL3, PFKP, ANKS1B, ABHD4, GTPBP2, PLXNA3, CREB3, NLRP12, PTPRK, RGN, GLUL, MMP13, CMYA5, CAMTAI, ABCA1, CDH1, EPHA10, DCHS1, OLFML1, SLC12A5, F8, ARHGAP22, LTBP3, PPP1R42, ADH5, REEP1, ADAMTS1, ATF5, ALDH1L1, ADAMTSL3, CSF1R, BSCL2, SLC15A2, CYP3A4, KIAA1644, ABCC6, GARS, ANTXRL, GGT7, P2RY4, IL1B, PRKAG2, TNFAIP3, VASP, FSTL1, KLHL38, SLC47A2, SLC5A5, FKBP14, MAGI2, GTPBP1, EXOC3L1, RAB37, KRT12, SLCO2B1, ADM2, DACT2, CHRD, ROBO3, MMP19, PTK7, PLEKHH1, FERMT1,SRPX2, TOX3, CTSS, MST1R, CCDC108, SEMA6C, AVPR1A, TSC22D4, FSTL3, ITGA2, PTGIS, COLEC12, NLN, FBXO32, CCDC153, DOCKIO, CYSTM1, FAM214A, CAND2, ARHGEF25, PTPLAD2, PAMR1, ULK2, PRODH, KRT8, TRIM55, KIAA1522, OPLAH, PREXI, LRP2, TBC1D2, INVS, ADAMTS12, MDM2, CSRNP1, RTP4, MED13L, NFKBIA, RGS12, LMNA, RIN1, TCN2, PDE7B, COL23A1, KIAA0141, AATK, IL1RAP, MXRA8, ZMIZ1, TMTC2, ISG15, MAP6, ACSL3, MKL2, ATXN1, WDFY2, CAPN2, ERRFI1, FARP1, HFE2, ZC3H12D, UAP1L1, RNF165, MPP5, SAT1, HBP1, AMPD2, HOMEZ, B3GNT2, STEAP4, PCDHAC2, COL4A3BP, TNS3, RNF169, AEBP1, TFE3, TTYH1, NEIL1, KIAA1033, MMP14, ACSL4, KLHL40, LPIN1, FGD1, XPC,TNFAIP2, CCDC92, DAB2, MTMR11, ZFYVE28, PC, ADIPOR2, MYODI, ZBTB33, METRNL, TBC1D2B, MFAP5, SCD, PPP1R3C, VPS4B, QPCT,CTSH, ARHGAP24, WDFY4, ROR2, ATP6V1B2, CTSZ, CXADR, MFSD2A, AVIL, XKRX, CHRNG, TIFA, TMCC3, SEMA4B, GDF10, PARD3, MAN2B1, PNPLA6, COL15A1, VPS41, TBC1D26, GHDC, HEY1, SCUBE3, MYLPF, MARCKSL1, RAB11FIP1, NTN1, GPT, GPD1, BAIAP2, MFI2, IPO13, ARHGEF28, ATP2A1, S0RBS2, AD API, TLE3, C11ORF54, CD58, MOG, DPYS15, HNRNPL, PDIA3, PLXNB3, HUNK, HEY1, IFI27L2, ARHGAP6, SP0N2, LFNG, HSD3B7, TMEM200B, ABAT, KCTD12, GSTM3, TNNI3, SEMA3E, HES1, UCP2, GALNT15, ADPRHL1, ANO8, SKAP2, COX7A2, DKK1, RABEPK, SHD, CEMIP, XYLT1, CPAMD8, PSMB8, FBP1, DLL1, TLCD1, ANKRD24, GALNT3, BCL2L13, THRAP3, SCARA5, MTTP, RANGRF, WDR83, ASL, PSMB10, SLC12A8, TM7SF2, ANXA3, LAMA3, FREM2, FAM60A, MYO16, ZEB2, STAC3, HYAL2, EMD, CDH2, CRAT, MEI, PLA2G6, LGALS9, DOK7, HIST1H1E, FRAT2, SLC35D1, BAG2, C14ORF159, SLC45A3, FMN2, STAC2, TTC28, SLC38A5, PTPRE, LSS, AMOTL2, CACNA1H, GPC5, SLC9A3R1, TPGS1, ARPP21, PLEKHG1, TUBA1A, EIF2AK2, MURC, JPH1, PPP2R3B, BPGM, ARHGAP8, TPCN2, ARSI, IER2, SPG20, TMEM198B, HGD, ALAS1, TGM1, and a combination thereof.60. The method of any one of embodiments 45-57 or 59, wherein the altered cell line and / or the altered expression profile comprises a change to a gene, a transcript, or a protein selected from the group consisting of ABCG2, SI, NDUFS8, ITGA5, CNTD1, PKHD1L1, PLXNB2, CASP10, FN1, ASAP2, IL13RA2, DAAM2, MCTP1, NUGGC, MEGF10, KIAA1324L, CPXM1, PHACTR4, FGF13, FLT1, PRICKLEI, ZEB1, SULF2, NET1, KIFAP3, HDAC9, DOPEY2, MAN2B2, TLE4, GARNL3, PFKP, ANKS1B, ABHD4, GTPBP2, PLXNA3, CREB3, NLRP12, PTPRK, RGN, GLUL, and a combination thereof.61. The composition of embodiment 60, wherein the change to the selected gene, transcript, or protein comprises a genetic variant comprising a deleterious effect on theresulting protein, compared to an effect of a non-variant gene of a corresponding or reference non-altered cell line or a reference genome.62. The composition of embodiment 60 or 61, wherein the change to the selected gene, transcript, or protein comprises a genetic variant comprising a frameshift, a nonsense, a stop codon, or a loss of function mutation.63. The composition of embodiment 61 or 62, wherein the deleterious effect comprises protein truncation, loss of protein function, and / or triggering of nonsense-mediated protein decay.64. The composition of any one of embodiments 60-63, wherein the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is upregulated by a change of about 0.5 to about 14 log fold, about 0.5 to about 12 log fold, 0.5 to about 10 log fold, about 0.5 to about 8 log fold, about 0.5 to about 6 log fold, about 0.5 to about 4 log fold, or about 0.5 to about 2 log fold, each inclusive, compared to a reference expression level of the selected gene.65. The composition of any one of embodiments 60-64, wherein the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is upregulated by a change of about 1.0 log fold, about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, 7.0 log fold, about 7.5 log fold, about 8.0 log fold, about 8.5 log fold, about 9.0 log fold, about 9.5 log fold, or about 10.0 log fold, compared to a reference expression level of the selected gene.66. The method of any one of embodiments 45-57 or 59, wherein the altered cell line and / or the altered expression profile comprises a change to a gene, a transcript, or a protein selected from the group consisting of GLUL, ABCG2, SI, MMP13, CMYA5, CAMTAI, ABCA1, CDH1, NDUFS8, EPHA10, DCHS1, OLFML1, ITGA5, SLC12A5, F8, CNTD1, PKHD1L1, ARHGAP22, LTBP3, PPP1R42, ADH5, REEP1, ADAMTS1, ATF5, ALDH1L1, ADAMTSL3, PLXNB2, CASP10, CSF1R, BSCL2, SLC15A2, CYP3A4, FN1, KIAA1644, ABCC6, GARS, ANTXRL, ASAP2, GGT7, GARS, P2RY4, ABCA1, IL1B, PRKAG2, TNFAIP3, VASP, FSTL1, IL13RA2, KLHL38, SLC47A2, SLC5A5, FKBP14, MAGI2, GTPBP1, DAAM2, EXOC3L1, RAB37, KRT12, SLCO2B1, ADM2, MCTP1, DACT2, NUGGC, CHRD, ROBO3, MMP19, PTK7, PLEKHH1, MEGF10, FERMT1, SRPX2, TOX3, CTSS, MST1R, CCDC108, SEMA6C, AVPR1A, TSC22D4, FSTL3, ITGA2, PTGIS, COLEC12, KIAA1324L, NLN, FBXO32, CCDC153, CPXM1, PHACTR4, FGF13, DOCK10, CYSTM1, FAM214A, CAND2, ARHGEF25, PTPLAD2, PAMR1, ULK2, PRODH, KRT8,TRIM55, KIAA1522, OPLAH, PREXI, LRP2, TBC1D2, INVS, FLT1, PRICKLEI, ADAMTS12, MDM2, CSRNP1, RTP4, MED13L, NFKBIA, RGS12, LMNA, RIN1, TCN2, PDE7B, COL23A1, KIAA0141, ANTXRL, AATK, ZEB1, IL1RAP, COL23A1, SULF2, MXRA8, ZMIZ1, TMTC2, KIFAP3, ISG15, MAP6, HDAC9, ACSL3, DOPEY2, MAN2B2, GARNL3, MKL2, ATXN1, WDFY2, CAPN2, ERRFI1, FARP1, HFE2, ZC3H12D, PFKP, ANKS1B, UAP1L1, ABHD4, RNF165, MPP5, SAT1, HBP1, AMPD2, HOMEZ, B3GNT2, GTPBP2, STEAP4, PCDHAC2, COL4A3BP, TNS3, RNF169, AEBP1, TFE3, TTYH1, NEIL1, KIAA1033, MMP14, ACSL4, KLHL40, LPIN1, FGD1, XPC, PLXNA3, TNFAIP2, CCDC92, DAB2, MTMR11, ZFYVE28, PC, ADIPOR2, MYODI, ZBTB33, METRNL, TBC1D2B, MFAP5, SCD, PPP1R3C, VPS4B, QPCT, METRNL, CTSH, CREB3, ARHGAP24, WDFY4, ROR2, ATP6V1B2, CTSZ, CXADR, MFSD2A, AVIL, XKRX, NLRP12, PTPRK, CHRNG, TIFA, TMCC3, SEMA4B, GDF10, PARD3, RGN, MAN2B1, PNPLA6, COL15A1, VPS41, TBC1D26, GHDC, ATHL1,, and a combination thereof.67. The composition of embodiment 66, wherein the change to the selected gene, transcript, or protein comprises a genetic variant comprising a non-deleterious effect on the resulting protein, compared an effect of a non-variant gene of a corresponding or reference non-altered cell line or a reference genome.68. The composition of embodiment 66 or 67, wherein the change to the selected gene, transcript, or protein comprises a genetic variant comprising an intragenic or an intron variant.69. The composition of embodiment 67 or 68, wherein the non-deleterious effect comprises an alteration or a change in effectiveness of the resulting protein.70. The composition of embodiment 69, wherein the effectiveness of the resulting protein is decreased.71. The composition of embodiment 69, wherein the effectiveness of the resulting protein is increased.72. The composition of any one of embodiments 66-71, wherein the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is upregulated by a change of about 0.5 to about 14 log fold, about 0.5 to about 12 log fold, 0.5 to about 10 log fold, about 0.5 to about 8 log fold, about 0.5 to about 6 log fold, about 0.5 to about 4 log fold, or about 0.5 to about 2 log fold, each inclusive, compared to a reference expression level of the selected gene.73. The composition of any one of embodiments 66-72, wherein the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is upregulated by a change of about 1.0 log fold, about 1.5 log fold, about 2.0 logfold, about 2.5 log fold, 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, 7.0 log fold, about 7.5 log fold, about 8.0 log fold, about 8.5 log fold, about 9.0 log fold, about 9.5 log fold, or about 10.0 log fold, compared to a reference expression level of the selected gene.74. The method of any one of embodiments 45-56 or 58-59, wherein he altered cell line and / or the altered expression profile comprises a change to a gene, a transcript, or a protein selected from the group consisting of HEY1, SCUBE3, MYLPF, MARCKSL1, RAB11FIP1, NTN1, GPT, GPD1, BAIAP2, MFI2, IPO13, ARHGEF28, ATP2A1, SORBS2, ADAP1, TLE3, C11ORF54, CD58, MOG, DPYS15, HNRNPL, PDIA3, PLXNB3, HUNK,, and a combination thereof.75. The composition of embodiment 74, wherein the selected gene, transcript, or protein comprises a genetic variant comprising a deleterious effect on the resulting protein, compared to a non-variant gene of a corresponding or reference non-altered cell line or a reference genome.76. The composition of embodiment 74 or 75, wherein the change to the selected gene, transcript, or protein comprises a genetic variant comprising a frameshift, a nonsense, a stop codon, or a loss of function mutation.77. The composition of embodiment 75 or 76, wherein the deleterious effect comprises protein truncation, loss of protein function, and / or triggering of nonsense-mediated protein decay.78. The composition of any one of embodiments 74-77, wherein the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is downregulated by a change of about 0.5 to about 14 log fold, about 0.5 to about 12 log fold, 0.5 to about 10 log fold, about 0.5 to about 8 log fold, about 0.5 to about 6 log fold, about 0.5 to about 4 log fold, or about 0.5 to about 2 log fold, each inclusive, compared to a reference expression level of the selected gene.79. The composition of any one of embodiments 74-78 wherein the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is downregulated by a change of about 1.0 log fold, about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, 7.0 log fold, about 7.5 log fold, about 8.0 log fold, about 8.5 log fold, about 9.0 log fold, about 9.5 log fold, or about 10.0 log fold, compared to a reference expression level of the selected gene.80. The method of any one of embodiments 45-56 or 58-59, wherein said modified expression profile comprises a modified expression profile of a gene, a transcript, or a protein selected from the group consisting of HEY1, IFI27L2, ARHGAP6, SPON2, SCUBE3, MYLPF, LFNG, HSD3B7, TMEM200B, AB AT, KCTD12, GSTM3, TNNI3, SEMA3E, HES1, UCP2, GALNT15, ADPRHL1, MARCKSL1, RAB11FIP1, ANO8, NTN1, SKAP2, GPT, COX7A2, DKK1, GPD1, BAIAP2, RABEPK, SHD, CEMIP, XYLT1, CPAMD8, PSMB8, FBP1, DLL1, MFI2, TLCD1, IPO13, ANKRD24, GALNT3, ARHGEF28, BCL2L13, THRAP3, SCARA5, MTTP, RANGRF, ATP2A1, WDR83, SORBS2, ASL, PSMB10, SLC12A8, TM7SF2, AD API, ANXA3, LAMA3, TLE3, FREM2, FAM60A, C11ORF54, MY016, CD58, ZEB2, STAC3, HYAL2, EMD, CDH2, CRAT, MEI, PLA2G6, LGALS9, DOK7, MOG, HIST1H1E, FRAT2, SLC35D1, BAG2, HNRNPL, C14ORF159, SLC45A3, FMN2, STAC2, TTC28, SLC38A5, PTPRE, LSS, AMOTL2, CACNA1H, GPC5, SLC9A3R1, TPGS1, ARPP21, PLEKHG1, TUBA1A, EIF2AK2, MURC, JPH1, PPP2R3B, BPGM, ARHGAP8, TPCN2, PDIA3, ARSI, IER2, PLXNB3, SPG20, TMEM198B, HUNK, HGD, ALAS1,, and a combination thereof.81. The composition of embodiment 80, wherein the change to the selected gene, transcript, or protein comprises a genetic variant comprising a non-deleterious effect on the resulting protein, compared an effect of a non-variant gene of a corresponding or reference non-altered cell line or a reference genome.82. The composition of embodiment 80 or 81 , wherein the change to the selected gene, transcript, or protein comprises a genetic variant comprising an intragenic or an intron variant.83. The composition of embodiment 81 or 82, wherein the non-deleterious effect comprises an alteration or a change in effectiveness of the resulting protein.84. The composition of embodiment 83, wherein the effectiveness of the resulting protein is decreased.85. The composition of embodiment 83, wherein the effectiveness of the resulting protein is increased.86. The composition of any one of embodiments 80-85, wherein the change to the selected gene, transcript, or protein a change in gene expression level, wherein the selected gene is do...

Claims

CLAIMSWhat is claimed is:

1. A composition, comprising an altered cell line that has an altered expression profile as compared to an expression profile of a corresponding non-altered cell line, wherein the altered cell line is a suspension cell line.

2. A composition, comprising an altered cell line that has an altered expression profile as compared to an expression profile of a reference non-altered cell line, wherein the altered cell like is a suspension cell line.

3. The composition of claim 1 or 2, wherein the altered expression profile comprises an altered gene expression profile and / or an altered phenotypic profile.

4. The composition of claim 3, wherein the altered phenotypic profile comprises of improved viability and stable growth rates in (1) non-adherent, suspension cell culture, (2) serum-free media cell culture, and / or (3) animal component-free media cell culture.

5. The composition of any one of claims 1-4, wherein the altered expression profile comprises an upregulated gene expression profile.

6. The composition of any one of claims 1-4, wherein the altered expression profile comprises a downregulated gene expression profile.

7. The composition of any one of claims 1-6, wherein the altered expression profile comprises a change to a gene, a transcript, or a protein selected from the group consisting of ABCG2, SI, NDUFS8, ITGA5, CNTD1, PKHD1L1, PLXNB2, CASP10, FN1, ASAP2, IL13RA2, DAAM2, MCTP1, NUGGC, MEGF10, KIAA1324L, CPXM1, PHACTR4, FGF13, FLT1, PRICKLEI, ZEB1, SULF2, NET1, KIFAP3, HDAC9, D0PEY2, MAN2B2, TLE4, GARNL3, PFKP, ANKS1B, ABHD4, GTPBP2, PLXNA3, CREB3, NLRP12, PTPRK, RGN, GLUL, MMP13, CMYA5, CAMTAI, ABCA1, CDH1, EPHA10, DCHS1, 0LFML1, SLC12A5, F8, ARHGAP22, LTBP3, PPP1R42, ADH5, REEP1, ADAMTS1, ATF5, ALDH1L1, ADAMTSL3, CSF1R, BSCL2, SLC15A2, CYP3A4, KIAA1644, ABCC6, GARS, ANTXRL, GGT7, P2RY4, IL1B, PRKAG2, TNFAIP3, VASP, FSTL1, KLHL38, SLC47A2, SLC5A5, FKBP14, MAGI2, GTPBP1, EX0C3L1, RAB37, KRT12, SLCO2B1, ADM2, DACT2, CHRD, R0B03, MMP19, PTK7, PLEKHH1, FERMT1, SRPX2, T0X3, CTSS, MST1R, CCDC108, SEMA6C, AVPR1A, TSC22D4, FSTL3, ITGA2, PTGIS, COLEC12, NLN, FBXO32, CCDC153, DOCKIO, CYSTM1, FAM214A, CAND2, ARHGEF25,PTPLAD2, PAMR1, ULK2, PRODH, KRT8, TRIM55, KIAA1522, OPLAH, PREXI, LRP2, TBC1D2, INVS, ADAMTS12, MDM2, CSRNP1, RTP4, MED13L, NFKBIA, RGS12, LMNA, RIN1, TCN2, PDE7B, COL23A1, KIAA0141, AATK, IL1RAP, MXRA8, ZMIZ1, TMTC2, ISG15, MAP6, ACSL3, MKL2, ATXN1, WDFY2, CAPN2, ERRFI1, FARP1, HFE2, ZC3H12D, UAP1L1, RNF165, MPP5, SAT1, HBP1, AMPD2, HOMEZ, B3GNT2, STEAP4, PCDHAC2, COL4A3BP, TNS3, RNF169, AEBP1, TFE3, TTYH1, NEIL1, KIAA1033, MMP14, ACSL4, KLHL40, LPIN1, FGD1, XPC,TNFAIP2, CCDC92, DAB2, MTMR11, ZFYVE28, PC, ADIPOR2, MYODI, ZBTB33, METRNL, TBC1D2B, MFAP5, SCD, PPP1R3C, VPS4B, QPCT, CTSH, ARHGAP24, WDFY4, ROR2, ATP6V1B2, CTSZ, CXADR, MFSD2A, AVIL, XKRX, CHRNG, TIFA, TMCC3, SEMA4B, GDF10, PARD3, MAN2B1, PNPLA6, COL15A1, VPS41, TBC1D26, GHDC, HEY1, SCUBE3, MYLPF, MARCKSL1, RAB11FIP1, NTN1, GPT, GPD1, BAIAP2, MFI2, IPO13, ARHGEF28, ATP2A1, SORBS2, AD API, TLE3, C11ORF54, CD58, MOG, DPYS15, HNRNPL, PDIA3, PLXNB3, HUNK, HEY1, IFI27L2, ARHGAP6, SPON2, LFNG, HSD3B7, TMEM200B, ABAT, KCTD12, GSTM3, TNNI3, SEMA3E, HES1, UCP2, GALNT15, ADPRHL1, ANO8, SKAP2, COX7A2, DKK1, RABEPK, SHD, CEMIP, XYLT1, CPAMD8, PSMB8, FBP1, DLL1, TLCD1, ANKRD24, GALNT3, BCL2L13, THRAP3, SCARA5, MTTP, RANGRF, WDR83, ASL, PSMB10, SLC12A8, TM7SF2, ANXA3, LAMA3, FREM2, FAM60A, MYO16, ZEB2, STAC3, HYAL2, EMD, CDH2, CRAT, MEI, PLA2G6, LGALS9, DOK7, HIST1H1E, FRAT2, SLC35D1, BAG2, C14ORF159, SLC45A3, FMN2, STAC2, TTC28, SLC38A5, PTPRE, LSS, AMOTL2, CACNA1H, GPC5, SLC9A3R1, TPGS1, ARPP21, PLEKHG1, TUBA1A, EIF2AK2, MURC, JPH1, PPP2R3B, BPGM, ARHGAP8, TPCN2, ARSI, IER2, SPG20, TMEM198B, HGD, ALAS1, TGM1, and a combination thereof.

8. The composition of claims any one of claims 1-5 or 7, wherein the altered expression profile comprises a change to a gene, a transcript, or a protein selected from the group consisting of ABCG2, SI, NDUFS8, ITGA5, CNTD1, PKHD1L1, PLXNB2, CASP10, FN1, ASAP2, IL13RA2, DAAM2, MCTP1, NUGGC, MEGF10, KIAA1324L, CPXM1, PHACTR4, FGF13, FLT1, PRICKLEI, ZEB1, SULF2, NET1, KIFAP3, HDAC9, DOPEY2, MAN2B2, TLE4, GARNL3, PFKP, ANKS1B, ABHD4, GTPBP2, PLXNA3, CREB3, NLRP12, PTPRK, RGN, GLUL, and a combination thereof.

9. The composition of claim 8, wherein the change to the selected gene, transcript, or protein comprises a genetic variant comprising a deleterious effect on the resulting protein,compared to an effect of a non-variant gene of a corresponding or reference non-altered cell line or a reference genome.

10. The composition of claim 8 or 9, wherein the change to the selected gene, transcript, or protein comprises a genetic variant comprising a frameshift, a nonsense, a stop codon, or a loss of function mutation.

11. The composition of claim 9 or 10, wherein the deleterious effect comprises protein truncation, loss of protein function, and / or triggering of nonsense-mediated protein decay.

12. The composition of any one of claims 8-11, wherein the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is upregulated by a change of about 0.5 to about 14 log fold, about 0.5 to about 12 log fold, 0.5 to about 10 log fold, about 0.5 to about 8 log fold, about 0.5 to about 6 log fold, about 0.5 to about 4 log fold, or about 0.5 to about 2 log fold, each inclusive, compared to a reference expression level of the selected gene.

13. The composition of any one of claims 8-12, wherein the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is upregulated by a change of about 1.0 log fold, about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, 7.0 log fold, about 7.5 log fold, about 8.0 log fold, about 8.5 log fold, about 9.0 log fold, about 9.5 log fold, or about 10.0 log fold, compared to a reference expression level of the selected gene.

14. The composition of any one of claims 1-5 or 7, wherein the altered expression profile comprises a change to a gene, a transcript, or a protein selected from the group consisting of GLUL, ABCG2, SI, MMP13, CMYA5, CAMTAI, ABCA1, CDH1, NDUFS8, EPHA10, DCHS1, OLFML1, ITGA5, SLC12A5, F8, CNTD1, PKHD1L1, ARHGAP22, LTBP3, PPP1R42, ADH5, REEP1, ADAMTS1, ATF5, ALDH1L1, ADAMTSL3, PLXNB2, CASP10, CSF1R, BSCL2, SLC15A2, CYP3A4, FN1, KIAA1644, ABCC6, GARS, ANTXRL, ASAP2, GGT7, GARS, P2RY4, ABCA1, IL1B, PRKAG2, TNFAIP3, VASP, FSTL1, IL13RA2, KLHL38, SLC47A2, SLC5A5, FKBP14, MAGI2, GTPBP1, DAAM2, EXOC3L1, RAB37, KRT12, SLCO2B1, ADM2, MCTP1, DACT2, NUGGC, CHRD, ROBO3, MMP19, PTK7, PLEKHH1, MEGF10, FERMT1, SRPX2, TOX3, CTSS, MST1R, CCDC108, SEMA6C, AVPR1A, TSC22D4, FSTL3, ITGA2, PTGIS, COLEC12, KIAA1324L, NLN, FBXO32, CCDC153, CPXM1, PHACTR4, FGF13, DOCK10, CYSTM1, FAM214A,CAND2, ARHGEF25, PTPLAD2, PAMR1, ULK2, PRODH, KRT8, TRIM55, KIAA1522, OPLAH, PREXI, LRP2, TBC1D2, INVS, FLT1, PRICKLEI, ADAMTS12, MDM2, CSRNP1, RTP4, MED13L, NFKBIA, RGS12, LMNA, RIN1, TCN2, PDE7B, COL23A1, KIAA0141, ANTXRL, AATK, ZEB1, IL1RAP, COL23A1, SULF2, MXRA8, ZMIZ1, TMTC2, KIFAP3, ISG15, MAP6, HDAC9, ACSL3, DOPEY2, MAN2B2, GARNL3, MKL2, ATXN1, WDFY2, CAPN2, ERRFI1, FARP1, HFE2, ZC3H12D, PFKP, ANKS1B, UAP1L1, ABHD4, RNF165, MPP5, SAT1, HBP1, AMPD2, HOMEZ, B3GNT2, GTPBP2, STEAP4, PCDHAC2, COL4A3BP, TNS3, RNF169, AEBP1, TFE3, TTYH1, NEIL1, KIAA1033, MMP14, ACSL4, KLHL40, LPIN1, FGD1, XPC, PLXNA3, TNFAIP2, CCDC92, DAB2, MTMR11, ZFYVE28, PC, ADIPOR2, MYODI, ZBTB33, METRNL, TBC1D2B, MFAP5, SCD, PPP1R3C, VPS4B, QPCT, METRNL, CTSH, CREB3, ARHGAP24, WDFY4, ROR2, ATP6V1B2, CTSZ, CXADR, MFSD2A, AVIL, XKRX, NLRP12, PTPRK, CHRNG, TIFA, TMCC3, SEMA4B, GDF10, PARD3, RGN, MAN2B1, PNPLA6, COL15A1, VPS41, TBC1D26, GHDC, ATHL1, and a combination thereof.

15. The composition of claim 14, wherein the change to the selected gene, transcript, or protein comprises a genetic variant comprising a non-deleterious effect on the resulting protein, compared an effect of a non-variant gene of a corresponding or reference non-altered cell line or a reference genome.

16. The composition of claim 14 or 15, wherein the change to the selected gene, transcript, or protein comprises a genetic variant comprising an intragenic or an intron variant.

17. The composition of claim 15 or 16, wherein the non-deleterious effect comprises an alteration or a change in effectiveness of the resulting protein.

18. The composition of claim 17, wherein the effectiveness of the resulting protein is decreased.

19. The composition of claim 17, wherein the effectiveness of the resulting protein is increased.

20. The composition of any one of claims 14-19, wherein the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is upregulated by a change of about 0.5 to about 14 log fold, about 0.5 to about 12 log fold, 0.5 to about 10 log fold, about 0.5 to about 8 log fold, about 0.5 to about 6 log fold, about0.5 to about 4 log fold, or about 0.5 to about 2 log fold, each inclusive, compared to a reference expression level of the selected gene.

21. The composition of any one of claims 14-20, wherein the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is upregulated by a change of about 1.0 log fold, about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, 7.0 log fold, about 7.5 log fold, about 8.0 log fold, about 8.5 log fold, about 9.0 log fold, about 9.5 log fold, or about 10.0 log fold, compared to a reference expression level of the selected gene.

22. The composition of any one of claims 1-4 or 6-7, wherein the altered expression profile comprises a change to a gene, a transcript, or a protein selected from the group consisting of HEY1, SCUBE3, MYLPF, MARCKSL1, RAB11FIP1, NTN1, GPT, GPD1, BAIAP2, MFI2, IPO13, ARHGEF28, ATP2A1, SORBS2, AD API, TLE3, Cl 1ORF54, CD58, MOG, DPYS15, HNRNPL, PDIA3, PLXNB3, HUNK, and a combination thereof.

23. The composition of claim 22, wherein the selected gene, transcript, or protein comprises a genetic variant comprising a deleterious effect on the resulting protein, compared to a non-variant gene of a corresponding or reference non-altered cell line or a reference genome.

24. The composition of claim 22 or 23, wherein the change to the selected gene, transcript, or protein comprises a genetic variant comprising a frameshift, a nonsense, a stop codon, or a loss of function mutation.

25. The composition of claim 23 or 24, wherein the deleterious effect comprises protein truncation, loss of protein function, and / or triggering of nonsense-mediated protein decay.

26. The composition of any one of claims 22-25, wherein the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is downregulated by a change of about 0.5 to about 14 log fold, about 0.5 to about 12 log fold, 0.5 to about 10 log fold, about 0.5 to about 8 log fold, about 0.5 to about 6 log fold, about 0.5 to about 4 log fold, or about 0.5 to about 2 log fold, each inclusive, compared to a reference expression level of the selected gene.

27. The composition of any one of claims 22-26, wherein the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is downregulated by a change of about 1.0 log fold, about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, 7.0 log fold, about 7.5 log fold, about 8.0 log fold, about 8.5 log fold, about 9.0 log fold, about 9.5 log fold, or about 10.0 log fold, compared to a reference expression level of the selected gene.

28. The composition of any one of claims 1-4 or 6-7, wherein the altered expression profile comprises a change to a gene, a transcript, or a protein selected from the group consisting of HEY1, IFI27L2, ARHGAP6, SPON2, SCUBE3, MYLPF, LFNG, HSD3B7, TMEM200B, ABAT, KCTD12, GSTM3, TNNI3, SEMA3E, HES1, UCP2, GALNT15, ADPRHL1, MARCKSL1, RAB11FIP1, AN08, NTN1, SKAP2, GPT, COX7A2, DKK1, GPD1, BAIAP2, RABEPK, SHD, CEMIP, XYLT1, CPAMD8, PSMB8, FBP1, DLL1, MFI2, TLCD1, IPO13, ANKRD24, GALNT3, ARHGEF28, BCL2L13, THRAP3, SCARA5, MTTP, RANGRF, ATP2A1, WDR83, SORBS2, ASL, PSMB10, SLC12A8, TM7SF2, AD API, ANXA3, LAMA3, TLE3, FREM2, FAM60A, C11ORF54, MY016, CD58, ZEB2, STAC3, HYAL2, EMD, CDH2, CRAT, MEI, PLA2G6, LGALS9, D0K7, MOG, HIST1H1E, FRAT2, SLC35D1, BAG2, HNRNPL, C14ORF159, SLC45A3, FMN2, STAC2, TTC28, SLC38A5, PTPRE, LSS, AM0TL2, CACNA1H, GPC5, SLC9A3R1, TPGS1, ARPP21, PLEKHG1, TUBA1A, EIF2AK2, MURC, JPH1, PPP2R3B, BPGM, ARHGAP8, TPCN2, PDIA3, ARSI, IER2, PLXNB3, SPG20, TMEM198B, HUNK, HGD, ALAS1, TGM1, and a combination thereof.

29. The composition of claim 28, wherein the change to the selected gene, transcript, or protein comprises a genetic variant comprising a non-deleterious effect on the resulting protein, compared an effect of a non-variant gene of a corresponding or reference non-altered cell line or a reference genome.

30. The composition of claim 28 or 29, wherein the change to the selected gene, transcript, or protein comprises a genetic variant comprising an intragenic or an intron variant.

31. The composition of claim 29 or 30, wherein the non-deleterious effect comprises an alteration or a change in effectiveness of the resulting protein.

32. The composition of claim 31, wherein the effectiveness of the resulting protein is decreased.

33. The composition of claim 31, wherein the effectiveness of the resulting protein is increased.

34. The composition of any one of claims 28-33, wherein the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is downregulated by a change of about 0.5 to about 14 log fold, about 0.5 to about 12 log fold, 0.5 to about 10 log fold, about 0.5 to about 8 log fold, about 0.5 to about 6 log fold, about 0.5 to about 4 log fold, or about 0.5 to about 2 log fold, each inclusive, compared to a reference expression level of the selected gene.

35. The composition of any one of claims 28-34, wherein the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is downregulated by a change of about 1.0 log fold, about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, 7.0 log fold, about 7.5 log fold, about 8.0 log fold, about 8.5 log fold, about 9.0 log fold, about 9.5 log fold, or about 10.0 log fold, compared to a reference expression level of the selected gene.

36. The composition of any one of claims 1-35, wherein the altered cell line has been altered with mutagenesis, chemical mutagens, physical mutagens, electromagnetic radiation, particle radiation, CRISPR, transfection, viruses, non-integrative nucleic acid molecules, or a combination thereof.

37. The composition of any one of claims 1-36, wherein the altered cell line has been altered with alkylating agents and azides.

38. The composition of any one of claims 1-37, wherein the altered cell line has been altered with alkylating agents selected from the group consisting of N-ethyl-N-nitrosourea (ENU), ethyl methanesulfonate (EMS), and a combination thereof.

39. The composition of any one of claims 1-36, wherein the altered cell line has been altered with electromagnetic radiation selected from the group consisting of gamma rays, x- rays, UV light, and a combination thereof.

40. The composition of any one of claims 1-36, wherein the altered cell line has been altered with particle radiation selected from the group consisting of fast neutrons, thermal neutrons, beta particles, alpha particles, and a combination thereof.

41. The composition of any one of claims 1-40, wherein the altered cell line, the nonaltered cell line, and / or the reference genome is derived from an aquatic species comprising at least one species selected from the group consisting of Bluefin tuna (Thunnus orientalis, Thunnus maccoyii, and Thunnus ihynnus), yellowfin tuna (Thunnus albacares), yellowtail (e.g., Seriola lalandi), mahi-mahi (Coryphaena hippurus). red snapper (Lutjanus campechanus). cod (e.g., Gadus morhua, Gadus Macrocephalus, Gadus ogac), flounder, halibut, herring, mackeral, pompano, salmon (Salmo salar), sea bass, Patagonian toothfish (Dissostichus eleginoides), squid, clams, lobster, crabs, scallops, shrimp, eel, bass (e.g., Micropterus salmoides), bluegill (Lepomis macrochirus), rainbow trout (Oncorhynchus rnykiss), tilapia (Oreochromis massambicus), and carp (e.g., Hypophthalmichthys molitrix).

42. The composition of any one of claims 1-41, wherein the altered cell line, the nonaltered cell line, and / or the reference genome is derived from an aquatic species comprising at least one species selected from the group consisting of northern Bluefin tuna (T. thynnus), albacore (T. alalunga), yellowfin tuna (T. albacares), southern Bluefin tuna (T. thynnus maccoyii), bigeye tuna (T. obesus), blackfin tuna (T. atlanticus), Pacific Bluefin tuna (Thunnus orientalis), and longtail tuna (T. tonggol).

43. The composition of any one of claims 1-40, wherein the altered cell line, the nonaltered cell line, and / or the reference genome is derived an aquatic species comprising at least one species selected from the group consisting of bass, flounder, hake, scup, smelt, rainbow trout, hardshell clam, blue crab, peekytoe crab, spanner crab, cuttlefish, Eastern oyster, Pacific oyster, anchovy, herring, lingcod, moi, orange roughy, Atlantic Ocean perch, Lake Victoria perch, yellow perch, European oyster, Dover sole, sturgeon, tilefish, wahoo, yellowtail, sea urchin, Atlantic mackerel, sardines, black sea bass, European sea bass, hybrid striped bass, bream, cod, drum, haddock, hoki, Alaska pollock, rockfish, pink salmon, snapper, tilapia, turbot, walleye, lake whitefish, wolffish, hardshell clam, surf clam, cockle, Jonah crab, snow crab, crayfish, bay scallop, Chinese white shrimp, sablefish, Atlantic salmon, coho salmon, skate, dungeness crab, king crab, blue mussel, greenshell mussel, pink shrimp, Escolar, chinook salmon, chum salmon, American shad, Arctic char, carp, catfish, dory, grouper, halibut, monkfish, pompano, abalone, conch, stone crab, American lobster, spiny lobster, octopus, black tiger shrimp, freshwater shrimp, gulf shrimp, Pacific white shrimp, squid, barramundi, cusk, dogfish, kingklip, mahi-mahi, opah, mako shark, swordfish, albacore tuna, yellowfin tuna, geoduck clam, squat lobster, sea scallop, rock shrimp, barracuda, Chilean sea bass, cobia,croaker, eel, blue marlin, mullet, sockeye salmon, Bluefin tuna, shrimp, crabs, lobster, and echinoderms (e.g. sea cucumbers and sea urchins).

44. The composition of any one of claims 1-43, wherein the altered cell line, the nonaltered cell line, and / or the reference genome is derived from Bluefin tuna (Thunnus orientalis, Thunnus maccoyii, and Thunnus ihynnus).

45. A method for generating an altered cell line, the method comprising(a) providing an adherent cell line or derivative thereof; and(b) subjecting the adherent cell line or derivative thereof to a process sufficient to generate an altered cell line comprising an altered expression profile that is different than an expression profile of a corresponding non-altered cell line.

46. A method for generating an altered cell line, the method comprising(a) providing an adherent cell line or derivative thereof; and(b) subjecting the adherent cell line or derivative thereof to a process sufficient to generate an altered cell line comprising an altered expression profile comprising:(1) an altered gene expression profile that is different than a gene expression profile of the adherent cell line or derivative used in (a) and / or a reference non-altered cell line; and / or(2) an altered phenotypic profile that is different than a phenotypic profile of the adherent cell line or derivative used in (a) and / or a reference non-altered cell line.

47. The composition of claim 46, wherein the altered phenotypic profile comprises of improved viability and stabilized growth rates in (1) non-adherent, suspension cell culture, (2) serum-free media cell culture, and / or (3) animal component-free media culture.

48. The method of any one of claims 45-47, wherein the altered cell line is a suspension cell line.

49. The method of any one of claims 45-47, wherein the altered cell line is an altered adherent cell line.

50. The method of any one of claims 45-49, wherein the subjecting in step (b) is performed in vitro.

51. The method of any one of claims 45-50, wherein the adherent cell line or derivative, the generated altered cell line, and / or the non-altered cell line is derived from an aquatic species.

52. The method of any one of claims 45-51, wherein the adherent cell line or derivative, the generated altered cell line, and / or the non-altered cell line is derived from an aquatic species comprising at least one species selected from the group consisting of Bluefin tuna (Thunnus orientalis and Thunnus thynnus), yellowfin tuna (Thunnus albacares), yellowtail (e.g., Seriola lalandi), mahi-mahi {Coryphaena hippurus), red snapper (Lutjanus campechanus), cod (e.g., Gadus morhua, Gadus Macrocephalus, Gadus ogac), flounder, halibut, herring, mackeral, pompano, salmon (Salmo salar), sea bass, Patagonian toothfish (Dissostichus eleginoides), squid, clams, lobster, crabs, scallops, shrimp, eel, bass (e.g., Micropterus salmoides), bluegill (Lepomis macrochirus), rainbow trout (Oncorhynchus mykiss), tilapia (Oreochromis massambicus), and carp (e.g., Hypophthalmichthys molitrix).

53. The method of any one of claims 45-52, wherein the adherent cell line or derivative, the generated altered cell line, and / or the non-altered cell line is derived from an aquatic species comprising at least one species selected from the group consisting of northern Bluefin tuna (T. thynnus), albacore (T. alalunga), yellowfin tuna (T. albacares), southern Bluefin tuna (T. thymus maccoyii), bigeye tuna (T. obesus), blackfin tuna (T. atlanticus), Pacific Bluefin tuna (Thunnus orientalis), and longtail tuna (T. tonggol).

54. The method of any one of claims 45-51, wherein the adherent cell line or derivative, the generated altered cell line, and / or the non-altered cell line is derived from an aquatic species comprising at least one species selected from the group consisting of bass, flounder, hake, scup, smelt, rainbow trout, hardshell clam, blue crab, peekytoe crab, spanner crab, cuttlefish, Eastern oyster, Pacific oyster, anchovy, herring, lingcod, moi, orange roughy, Atlantic Ocean perch, Lake Victoria perch, yellow perch, European oyster, Dover sole, sturgeon, tilefish, wahoo, yellowtail, sea urchin, Atlantic mackerel, sardines, black sea bass, European sea bass, hybrid striped bass, bream, cod, drum, haddock, hoki, Alaska pollock, rockfish, pink salmon, snapper, tilapia, turbot, walleye, lake whitefish, wolffish, hardshell clam, surf clam, cockle, Jonah crab, snow crab, crayfish, bay scallop, Chinese white shrimp, sablefish, Atlantic salmon, coho salmon, skate, dungeness crab, king crab, blue mussel, greenshell mussel, pink shrimp, Escolar, chinook salmon, chum salmon, American shad, Arctic char, carp, catfish, dory, grouper, halibut, monkfish, pompano, abalone, conch, stone crab,American lobster, spiny lobster, octopus, black tiger shrimp, freshwater shrimp, gulf shrimp, Pacific white shrimp, squid, barramundi, cusk, dogfish, kingklip, mahi-mahi, opah, mako shark, swordfish, albacore tuna, yellowfin tuna, geoduck clam, squat lobster, sea scallop, rock shrimp, barracuda, Chilean sea bass, cobia, croaker, eel, blue marlin, mullet, sockeye salmon, Bluefin tuna, shrimp, crabs, lobster, and echinoderms (e.g. sea cucumbers and sea urchins).

55. The method of any one of claims 45-54, wherein the process sufficient to generate the altered cell line comprises contacting the adherent cell line or derivative thereof with a chemical mutagen, a physical mutagen, electromagnetic radiation, particle radiation, a virus, non-integrative nucleic acid molecules, or a combination thereof.

56. The method of any one of claims 45-54, wherein the process sufficient to generate the altered cell line comprises contacting the adherent cell line or derivative thereof with an heterologous gene including a gene regulating moiety, wherein the gene regulating moiety is configured to regulate and / or modify an expression of a target gene, a target transcript, or a target protein of the adherent cell line or derivative thereof, thereby effecting the altered expression profile of the target gene, the transcript, or the target protein in the altered cell line as compared to the corresponding or reference non-altered cell line.

57. The method of any one of claims 45-56, wherein the altered expression profile comprises an upregulated gene expression profile.

58. The method of any one of claims 45-56, wherein the altered expression profile comprises a downregulated gene expression profile.

59. The method of any one of claims 45-58, wherein the altered cell line and / or the altered expression profile comprises a change to a gene, a transcript, or a protein selected from the group consisting of ABCG2, SI, NDUFS8, ITGA5, CNTD1, PKHD1L1, PLXNB2, CASP10, FN1, ASAP2, IL13RA2, DAAM2, MCTP1, NUGGC, MEGF10, KIAA1324L, CPXM1, PHACTR4, FGF13, FLT1, PRICKLEI, ZEB1, SULF2, NET1, KIFAP3, HDAC9, D0PEY2, MAN2B2, TLE4, GARNL3, PFKP, ANKS1B, ABHD4, GTPBP2, PLXNA3, CREB3, NLRP12, PTPRK, RGN, GLUL, MMP13, CMYA5, CAMTAI, ABCA1, CDH1, EPHA10, DCHS1, 0LFML1, SLC12A5, F8, ARHGAP22, LTBP3, PPP1R42, ADH5, REEP1, ADAMTS1, ATF5, ALDH1L1, ADAMTSL3, CSF1R, BSCL2, SLC15A2, CYP3A4, KIAA1644, ABCC6, GARS, ANTXRL, GGT7, P2RY4, IL1B, PRKAG2, TNFAIP3, VASP, FSTL1, KLHL38, SLC47A2, SLC5A5, FKBP14, MAGI2, GTPBP1, EX0C3L1, RAB37, KRT12, SLCO2B1, ADM2, DACT2, CHRD, R0B03, MMP19, PTK7, PLEKHH1, FERMT1,SRPX2, T0X3, CTSS, MST1R, CCDC108, SEMA6C, AVPR1A, TSC22D4, FSTL3, ITGA2, PTGIS, C0LEC12, NLN, FBXO32, CCDC153, DOCKIO, CYSTM1, FAM214A, CAND2, ARHGEF25, PTPLAD2, PAMR1, ULK2, PRODH, KRT8, TRIM55, KIAA1522, OPLAH, PREXI, LRP2, TBC1D2, INVS, ADAMTS12, MDM2, CSRNP1, RTP4, MED13L, NFKBIA, RGS12, LMNA, RIN1, TCN2, PDE7B, COL23A1, KIAA0141, AATK, IL1RAP, MXRA8, ZMIZ1, TMTC2, ISG15, MAP6, ACSL3, MKL2, ATXN1, WDFY2, CAPN2, ERRFI1, FARP1, HFE2, ZC3H12D, UAP1L1, RNF165, MPP5, SAT1, HBP1, AMPD2, HOMEZ, B3GNT2, STEAP4, PCDHAC2, COL4A3BP, TNS3, RNF169, AEBP1, TFE3, TTYH1, NEIL1, KIAA1033, MMP14, ACSL4, KLHL40, LPIN1, FGD1, XPC,TNFAIP2, CCDC92, DAB2, MTMR11, ZFYVE28, PC, ADIPOR2, MYODI, ZBTB33, METRNL, TBC1D2B, MFAP5, SCD, PPP1R3C, VPS4B, QPCT,CTSH, ARHGAP24, WDFY4, ROR2, ATP6V1B2, CTSZ, CXADR, MFSD2A, AVIL, XKRX, CHRNG, TIFA, TMCC3, SEMA4B, GDF10, PARD3, MAN2B1, PNPLA6, COL15A1, VPS41, TBC1D26, GHDC, HEY1, SCUBE3, MYLPF, MARCKSL1, RAB11FIP1, NTN1, GPT, GPD1, BAIAP2, MFI2, IPO13, ARHGEF28, ATP2A1, SORBS2, AD API, TLE3, C11ORF54, CD58, MOG, DPYS15, HNRNPL, PDIA3, PLXNB3, HUNK, HEY1, IFI27L2, ARHGAP6, SPON2, LFNG, HSD3B7, TMEM200B, ABAT, KCTD12, GSTM3, TNNI3, SEMA3E, HES1, UCP2, GALNT15, ADPRHL1, ANO8, SKAP2, COX7A2, DKK1, RABEPK, SHD, CEMIP, XYLT1, CPAMD8, PSMB8, FBP1, DLL1, TLCD1, ANKRD24, GALNT3, BCL2L13, THRAP3, SCARA5, MTTP, RANGRF, WDR83, ASL, PSMB10, SLC12A8, TM7SF2, ANXA3, LAMA3, FREM2, FAM60A, MYO16, ZEB2, STAC3, HYAL2, EMD, CDH2, CRAT, MEI, PLA2G6, LGALS9, DOK7, HIST1H1E, FRAT2, SLC35D1, BAG2, C14ORF159, SLC45A3, FMN2, STAC2, TTC28, SLC38A5, PTPRE, LSS, AMOTL2, CACNA1H, GPC5, SLC9A3R1, TPGS1, ARPP21, PLEKHG1, TUBA1A, EIF2AK2, MURC, JPH1, PPP2R3B, BPGM, ARHGAP8, TPCN2, ARSI, IER2, SPG20, TMEM198B, HGD, ALAS1, TGM1, and a combination thereof.

60. The method of any one of claims 45-57 or 59, wherein the altered cell line and / or the altered expression profile comprises a change to a gene, a transcript, or a protein selected from the group consisting of ABCG2, SI, NDUFS8, ITGA5, CNTD1, PKHD1L1, PLXNB2, CASP10, FN1, ASAP2, IL13RA2, DAAM2, MCTP1, NUGGC, MEGF10, KIAA1324L, CPXM1, PHACTR4, FGF13, FLT1, PRICKLEI, ZEB1, SULF2, NET1, KIFAP3, HDAC9, DOPEY2, MAN2B2, TLE4, GARNL3, PFKP, ANKS1B, ABHD4, GTPBP2, PLXNA3, CREB3, NLRP12, PTPRK, RGN, GLUL, and a combination thereof.

61. The composition of claim 60, wherein the change to the selected gene, transcript, or protein comprises a genetic variant comprising a deleterious effect on the resulting protein, compared to an effect of a non-variant gene of a corresponding or reference non-altered cell line or a reference genome.

62. The composition of claim 60 or 61, wherein the change to the selected gene, transcript, or protein comprises a genetic variant comprising a frameshift, a nonsense, a stop codon, or a loss of function mutation.

63. The composition of claim 61 or 62, wherein the deleterious effect comprises protein truncation, loss of protein function, and / or triggering of nonsense-mediated protein decay.

64. The composition of any one of claims 60-63, wherein the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is upregulated by a change of about 0.5 to about 14 log fold, about 0.5 to about 12 log fold, 0.5 to about 10 log fold, about 0.5 to about 8 log fold, about 0.5 to about 6 log fold, about 0.5 to about 4 log fold, or about 0.5 to about 2 log fold, each inclusive, compared to a reference expression level of the selected gene.

65. The composition of any one of claims 60-64, wherein the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is upregulated by a change of about 1.0 log fold, about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, 7.0 log fold, about 7.5 log fold, about 8.0 log fold, about 8.5 log fold, about 9.0 log fold, about 9.5 log fold, or about 10.0 log fold, compared to a reference expression level of the selected gene.

66. The method of any one of claims 45-57 or 59, wherein the altered cell line and / or the altered expression profile comprises a change to a gene, a transcript, or a protein selected from the group consisting of GLUL, ABCG2, SI, MMP13, CMYA5, CAMTAI, ABCA1, CDH1, NDUFS8, EPHA10, DCHS1, OLFML1, ITGA5, SLC12A5, F8, CNTD1, PKHD1L1, ARHGAP22, LTBP3, PPP1R42, ADH5, REEP1, ADAMTS1, ATF5, ALDH1L1, ADAMTSL3, PLXNB2, CASP10, CSF1R, BSCL2, SLC15A2, CYP3A4, FN1, KIAA1644, ABCC6, GARS, ANTXRL, ASAP2, GGT7, GARS, P2RY4, ABCA1, IL1B, PRKAG2, TNFAIP3, VASP, FSTL1, IL13RA2, KLHL38, SLC47A2, SLC5A5, FKBP14, MAGI2, GTPBP1, DAAM2, EXOC3L1, RAB37, KRT12, SLCO2B1, ADM2, MCTP1, DACT2,NUGGC, CHRD, R0B03, MMP19, PTK7, PLEKHH1, MEGF10, FERMT1, SRPX2, TOX3, CTSS, MST1R, CCDC1O8, SEMA6C, AVPR1A, TSC22D4, FSTL3, ITGA2, PTGIS, COLEC12, KIAA1324L, NLN, FBXO32, CCDC153, CPXM1, PHACTR4, FGF13, DOCKIO, CYSTM1, FAM214A, CAND2, ARHGEF25, PTPLAD2, PAMR1, ULK2, PRODH, KRT8, TRIM55, KIAA1522, OPLAH, PREXI, LRP2, TBC1D2, INVS, FLT1, PRICKLEI, ADAMTS12, MDM2, CSRNP1, RTP4, MED13L, NFKBIA, RGS12, LMNA, RIN1, TCN2, PDE7B, COL23A1, KIAA0141, ANTXRL, AATK, ZEB1, IL1RAP, COL23A1, SULF2, MXRA8, ZMIZ1, TMTC2, KIFAP3, ISG15, MAP6, HDAC9, ACSL3, DOPEY2, MAN2B2, GARNL3, MKL2, ATXN1, WDFY2, CAPN2, ERRFI1, FARP1, HFE2, ZC3H12D, PFKP, ANKS1B, UAP1L1, ABHD4, RNF165, MPP5, SAT1, HBP1, AMPD2, HOMEZ, B3GNT2, GTPBP2, STEAP4, PCDHAC2, COL4A3BP, TNS3, RNF169, AEBP1, TFE3, TTYH1, NEIL1, KIAA1033, MMP14, ACSL4, KLHL40, LPIN1, FGD1, XPC, PLXNA3, TNFAIP2, CCDC92, DAB2, MTMR11, ZFYVE28, PC, ADIPOR2, MYODI, ZBTB33, METRNL, TBC1D2B, MFAP5, SCD, PPP1R3C, VPS4B, QPCT, METRNL, CTSH, CREB3, ARHGAP24, WDFY4, ROR2, ATP6V1B2, CTSZ, CXADR, MFSD2A, AVIL, XKRX, NLRP12, PTPRK, CHRNG, TIFA, TMCC3, SEMA4B, GDF10, PARD3, RGN, MAN2B1, PNPLA6, COL15A1, VPS41, TBC1D26, GHDC, ATHL1,, and a combination thereof.

67. The composition of claim 66, wherein the change to the selected gene, transcript, or protein comprises a genetic variant comprising a non-deleterious effect on the resulting protein, compared an effect of a non-variant gene of a corresponding or reference non-altered cell line or a reference genome.

68. The composition of claim 66 or 67, wherein the change to the selected gene, transcript, or protein comprises a genetic variant comprising an intragenic or an intron variant.

69. The composition of claim 67 or 68, wherein the non-deleterious effect comprises an alteration or a change in effectiveness of the resulting protein.

70. The composition of claim 69, wherein the effectiveness of the resulting protein is decreased.

71. The composition of claim 69, wherein the effectiveness of the resulting protein is increased.

72. The composition of any one of claims 66-71, wherein the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selectedgene is upregulated by a change of about 0.5 to about 14 log fold, about 0.5 to about 12 log fold, 0.5 to about 10 log fold, about 0.5 to about 8 log fold, about 0.5 to about 6 log fold, about 0.5 to about 4 log fold, or about 0.5 to about 2 log fold, each inclusive, compared to a reference expression level of the selected gene.

73. The composition of any one of claims 66-72, wherein the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is upregulated by a change of about 1.0 log fold, about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, 7.0 log fold, about 7.5 log fold, about 8.0 log fold, about 8.5 log fold, about 9.0 log fold, about 9.5 log fold, or about 10.0 log fold, compared to a reference expression level of the selected gene.

74. The method of any one of claims 45-56 or 58-59, wherein he altered cell line and / or the altered expression profile comprises a change to a gene, a transcript, or a protein selected from the group consisting of HEY1, SCUBE3, MYLPF, MARCKSL1, RAB11FIP1, NTN1, GPT, GPD1, BAIAP2, MFI2, IPO13, ARHGEF28, ATP2A1, SORBS2, ADAP1, TLE3, C11ORF54, CD58, MOG, DPYS15, HNRNPL, PDIA3, PLXNB3, HUNK,, and a combination thereof.

75. The composition of claim 74, wherein the selected gene, transcript, or protein comprises a genetic variant comprising a deleterious effect on the resulting protein, compared to a non-variant gene of a corresponding or reference non-altered cell line or a reference genome.

76. The composition of claim 74 or 75, wherein the change to the selected gene, transcript, or protein comprises a genetic variant comprising a frameshift, a nonsense, a stop codon, or a loss of function mutation.

77. The composition of claim 75 or 76, wherein the deleterious effect comprises protein truncation, loss of protein function, and / or triggering of nonsense-mediated protein decay.

78. The composition of any one of claims 74-77, wherein the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is downregulated by a change of about 0.5 to about 14 log fold, about 0.5 to about 12 log fold, 0.5 to about 10 log fold, about 0.5 to about 8 log fold, about 0.5 to about 6 log fold, about0.5 to about 4 log fold, or about 0.5 to about 2 log fold, each inclusive, compared to a reference expression level of the selected gene.

79. The composition of any one of claims 74-78 wherein the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is downregulated by a change of about 1.0 log fold, about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, 7.0 log fold, about 7.5 log fold, about 8.0 log fold, about 8.5 log fold, about 9.0 log fold, about 9.5 log fold, or about 10.0 log fold, compared to a reference expression level of the selected gene.

80. The method of any one of claims 45-56 or 58-59, wherein said modified expression profile comprises a modified expression profile of a gene, a transcript, or a protein selected from the group consisting of HEY1, IFI27L2, ARHGAP6, SPON2, SCUBE3, MYLPF, LFNG, HSD3B7, TMEM200B, ABAT, KCTD12, GSTM3, TNNI3, SEMA3E, HES1, UCP2, GALNT15, ADPRHL1, MARCKSL1, RAB11FIP1, AN08, NTN1, SKAP2, GPT, COX7A2, DKK1, GPD1, BAIAP2, RABEPK, SHD, CEMIP, XYLT1, CPAMD8, PSMB8, FBP1, DLL1, MFI2, TLCD1, IPO13, ANKRD24, GALNT3, ARHGEF28, BCL2L13, THRAP3, SCARA5, MTTP, RANGRF, ATP2A1, WDR83, SORBS2, ASL, PSMB10, SLC12A8, TM7SF2, AD API, ANXA3, LAMA3, TLE3, FREM2, FAM60A, C11ORF54, MY016, CD58, ZEB2, STAC3, HYAL2, EMD, CDH2, CRAT, MEI, PLA2G6, LGALS9, D0K7, MOG, HIST1H1E, FRAT2, SLC35D1, BAG2, HNRNPL, C14ORF159, SLC45A3, FMN2, STAC2, TTC28, SLC38A5, PTPRE, LSS, AM0TL2, CACNA1H, GPC5, SLC9A3R1, TPGS1, ARPP21, PLEKHG1, TUBA1A, EIF2AK2, MURC, JPH1, PPP2R3B, BPGM, ARHGAP8, TPCN2, PDIA3, ARSI, IER2, PLXNB3, SPG20, TMEM198B, HUNK, HGD, ALAS1,, and a combination thereof.

81. The composition of claim 80, wherein the change to the selected gene, transcript, or protein comprises a genetic variant comprising a non-deleterious effect on the resulting protein, compared an effect of a non-variant gene of a corresponding or reference non-altered cell line or a reference genome.

82. The composition of claim 80 or 81, wherein the change to the selected gene, transcript, or protein comprises a genetic variant comprising an intragenic or an intron variant.

83. The composition of claim 81 or 82, wherein the non-deleterious effect comprises an alteration or a change in effectiveness of the resulting protein.

84. The composition of claim 83, wherein the effectiveness of the resulting protein is decreased.

85. The composition of claim 83, wherein the effectiveness of the resulting protein is increased.

86. The composition of any one of claims 80-85, wherein the change to the selected gene, transcript, or protein a change in gene expression level, wherein the selected gene is downregulated by a change of about 0.5 to about 14 log fold, about 0.5 to about 12 log fold, 0.5 to about 10 log fold, about 0.5 to about 8 log fold, about 0.5 to about 6 log fold, about 0.5 to about 4 log fold, or about 0.5 to about 2 log fold, each inclusive, compared to a reference expression level of the selected gene.

87. The composition of any one of claims 80-86, wherein the change to the selected gene, transcript, or protein comprises a change in gene expression level, wherein the selected gene is downregulated by a change of about 1.0 log fold, about 1.5 log fold, about 2.0 log fold, about 2.5 log fold, 3.0 log fold, about 3.5 log fold, about 4.0 log fold, about 4.5 log fold, 5.0 log fold, about 5.5 log fold, about 6.0 log fold, about 6.5 log fold, 7.0 log fold, about 7.5 log fold, about 8.0 log fold, about 8.5 log fold, about 9.0 log fold, about 9.5 log fold, or about 10.0 log fold, compared to a reference expression level of the selected gene.

88. The method of claim 55, wherein the electromagnetic radiation is selected from the group consisting of gamma ray, x-rays, UV light and a combination thereof.

89. The method of claim 55, wherein the chemical mutagens is selected from the group consisting of alkylating agents, azides, and a combination thereof.

90. The method of claim 55, wherein the particle radiation is selected from the group consisting of fast neutrons, thermal neutrons, beta particles, alpha particles and a combination thereof.

91. The method of claim 56, wherein the gene regulating moiety is an endonuclease.

92. The method of claim 91, wherein the endonuclease is a clustered regularly interspaced short palindromic repeats (CRISPR)-associated (CAS) endonuclease.

93. The method of any one of claims 45-54, wherein the process sufficient to generate the altered cell line comprises contacting the adherent cell line with a vector construct carryinga heterologous gene, wherein expression of the heterologous gene effects a modified expression profile of the altered cell line.

94. The method of claim 93, wherein the vector construct comprises a DNA vector.

95. The method of claim 93, wherein the vector construct comprises an RNA vector.

96. The method of claim 93, wherein the vector construct is a non-viral vector selected from the group consisting of a cosmid, a yeast artificial chromosome, a bacterial artificial chromosome, a shuttle vector, a plasmid vector, a secretion vector, and any combination thereof.

97. The method of claim 93, wherein the vector construct is a viral vector selected from the group consisting of a retrovirus vector, an adeno-associated virus vector, an adenovirus vector, a herpesvirus vector, and a poxvirus vector.

98. The method of any one of claims 45-54, wherein the process sufficient to generate an altered cell line comprises forced, transient, non-integrative gene expression using various nucleic acid molecules, comprising contacting the adherent cell line with messenger ribonucleic acid (mRNA), complementary deoxyribonucleic acid (cDNA), micro RNA (miRNA), transfer RNA (tRNA), silencing RNA (siRNA), or any variants, combinations, or analogs thereof, wherein delivery of the nucleic acid molecules into the cell are not integrated into the genome of the cell, and wherein delivery of the nucleic acid molecules effects a modified expression profile in the altered cell.

99. The method of any one of claims 45-54, wherein the process sufficient to generate an altered cell line comprises altering, silencing, attenuating, and / or knocking out a gene or genetic construct to effect a modified expression profile of the altered cell line.

100. The method of any one of claims 45-54, wherein the process sufficient to generate an altered cell line comprises mutating a nucleic acid sequence of the adherent cell line using a mutagenesis technique.

101. The method of claim 100, wherein the mutagenesis technique comprises site- directed mutagenesis using error-prone PCR or oligonucleotide-directed mutagenesis.

Images